From owner-chemistry@ccl.net Mon Feb 7 03:25:00 2011 From: "A VM fray.gory:-:gmail.com" To: CCL Subject: CCL:G: gar2ped Message-Id: <-43886-110207032217-6751-Z61SuHXCi5AZ+H2a49CtkA-#-server.ccl.net> X-Original-From: A VM Content-Type: multipart/alternative; boundary=0016367fb2c7922b96049bacedfe Date: Mon, 7 Feb 2011 02:22:09 -0600 MIME-Version: 1.0 Sent to CCL by: A VM [fray.gory===gmail.com] --0016367fb2c7922b96049bacedfe Content-Type: text/plain; charset=ISO-8859-1 Hello, I dont have access to any version of Gaussian, but I compiled successfully the binary for gar2ped I dont know if it works, please check https://sites.google.com/site/alvarovazquezmayagoitia/compiling Regards, Alvaro On Sun, Feb 6, 2011 at 10:40 PM, sobereva sobjubao]|[yahoo.com.cn < owner-chemistry]^[ccl.net> wrote: > > Sent to CCL by: sobereva [sobjubao**yahoo.com.cn] > Hello, > > Although gar2ped is an very old software, I found gar2ped still works > properly for Gaussian03/09. > > I've tried compiling gar2ped by gfortran and ifort before but never > succeeded. If the operation system you used is not restricted to linux, I > suggest you compiling gar2ped by Compaq visual fortran (the version I used > is 6.5), I found it is very easy and changing any code is not required. Just > build a new project in CVF, drag pullarc.f to project and compile it to > pullarc.exe, then clean up the project, drag all other files to project and > compile them to gar2ped.exe, Makefile is no use in the compilation. The > generated executable files work well. > > Tian Lu > > --- On Mon, 2/7/11, Brian Salter-Duke Brian.Salter-Duke/amonash.edu ccl.net> wrote: > > > From: Brian Salter-Duke Brian.Salter-Duke/amonash.edu ccl.net> > > Subject: CCL:G: gar2ped > > To: "Lu, Tian " > > Date: Monday, February 7, 2011, 6:08 AM > > > > Sent to CCL by: Brian Salter-Duke > > [Brian.Salter-Duke|,|monash.edu] > > On Sun, Feb 06, 2011 at 10:06:16AM -0500, Jason Swails > > swails!A!qtp.ufl.edu wrote: > > > Install g77 on your system (gfortran will not work to > > compile it) and then > > > create a link to g77 called "f77" that is placed > > somewhere in your PATH. > > > ifort also works to compile gar2ped, so if you have > > ifort you can create a > > > link to ifort called "f77" somewhere in your path > > instead. Then just type > > > "make" in the gar2ped directory. (I believe > > pgf77 would also work if you > > > have that, but I couldn't verify it since I don't have > > access to it). > > > > I was puzzled that gfortran does not work, so I had a look > > at it. There > > is an error in the makefile. The first line sets FFLAGS but > > it is not > > used, while CFLAGS is used but not set. Change CFLAGS near > > the bottom > > to FLAGS. Then I found that setting:- > > > > FFLAGS = -std=legacy -fd-lines-as-code > > > > gets rid of all errors except one. -std=legacy gets over > > the non > > standard do loop in animate. -fd-lines-as-code gets over > > the objection > > to lines starting with "D" in column 1. That leaves a > > problem with > > format($,' .. in main.f. I just removed the "$,". It then > > compiles but > > it does not link. It can not find subroutine filnam. Now I > > am stuck. Any > > thoughts. > > > > This is very old code and it probably only works for G94. > > There was a > > change in format of the coordinates in the output file > > going from G94 to > > G98. I got it from CCL and it is dated "13-Dec-1996 12:00". > > Is there > > anything more recent? > > > > Cheers, Brian. > > > > > To use it, look at the README file included in the the > > source code. > > > > > > Hope this helps, > > > Jason > > > > > > On Sun, Feb 6, 2011 at 8:20 AM, neeraj misra > > neerajmisra++hotmail.com < > > > owner-chemistry{=}ccl.net> wrote: > > > > > > > > > > > Sent to CCL by: "neeraj misra" > > [neerajmisra(a)hotmail.com] > > > > DEAR MEMBERS, > > > > > > COULD ANYONE TELL ME HOW TO INSTALL GAR2PED PRPGRAM ON > > FEDORA > > > > CORE14..AND HOW TO RUN IT TOO...MY OBJECT IS TO > > CALCULATE THE POTENTIAL > > > > ENERGY DISTRIBUTION.. > > > > > > > > THANKS> > > > > > > > > > > > > > > > > > > > > -- > > > > Jason M. Swails > > > > Quantum Theory Project, > > > > University of Florida > > > > Ph.D. Graduate Student > > > > 352-392-4032 > > > > -- > > Brian Salter-Duke (Brian Duke) > > Brian.Salter-Duke:monash.edu > > > > Honorary Researcher Fellow > > Monash Institute > > of Pharmaceutical Sciences, > > Monash University Parkville Campus, > > VIC 3052, Australia. > > > > > > > > -= This is automatically added to each message by the > > mailing script =- > > To recover the email address of the author of the message, > > please change > > the strange characters on the top line to the :: sign. You > > can also> > > E-mail to subscribers: CHEMISTRY::ccl.net > > or use: > > > > > E-mail to administrators: CHEMISTRY-REQUEST::ccl.net > > or use> > > --0016367fb2c7922b96049bacedfe Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hello,

I dont have access to any version of G= aussian, but I compiled successfully the binary for gar2ped I dont know if = it works, please
check


Regards,

Alvaro
On Sun, Feb 6, 2011 at 10:40 PM, sobereva sobju= bao]|[yahoo.com.cn &l= t;owner-chemistry]^[ccl.net>= ; wrote:

Sent to CCL by: sobereva [sobjubao**yahoo.com.cn]
Hello,

Although gar2ped is an very old software, I found gar2ped still works prope= rly for Gaussian03/09.

I've tried compiling gar2ped by gfortran and ifort before but never suc= ceeded. If the operation system you used is not restricted to linux, I sugg= est you compiling gar2ped by Compaq visual fortran (the version I used is 6= .5), I found it is very easy and changing any code is not required. Just bu= ild a new project in CVF, drag pullarc.f to project and compile it to pulla= rc.exe, then clean up the project, drag all other files to project and comp= ile them to gar2ped.exe, Makefile is no use in the compilation. The generat= ed executable files work well.

Tian Lu

--- On Mon, 2/7/11, Brian Salter-Duke Brian.Salter-Duke/amonash.edu <owner-chemistry::ccl.net> wrote:

> From: Brian Salter-Duke Brian.Salter-Duke/amonash.edu <owner-chemistry::ccl.net>
> Subject: CCL:G: gar2ped
> To: "Lu, Tian " <sobjubao::yahoo.com.cn>
> Date: Monday, February 7, 2011, 6:08 AM
>
> Sent to CCL by: Brian Salter-Duke
> [Brian.Salter-Duke|,|m= onash.edu]
> On Sun, Feb 06, 2011 at 10:06:16AM -0500, Jason Swails
> swails!A!qtp.ufl.edu<= /a> wrote:
> > Install g77 on your system (gfortran will not work to
> compile it) and then
> > create a link to g77 called "f77" that is placed
> somewhere in your PATH.
> > ifort also works to compile gar2ped, so if you have
> ifort you can create a
> > link to ifort called "f77" somewhere in your path
> instead.=A0 Then just type
> > "make" in the gar2ped directory.=A0 (I believe
> pgf77 would also work if you
> > have that, but I couldn't verify it since I don't have > access to it).
>
> I was puzzled that gfortran does not work, so I had a look
> at it. There
> is an error in the makefile. The first line sets FFLAGS but
> it is not
> used, while CFLAGS is used but not set. Change CFLAGS near
> the bottom
> to FLAGS. Then I found that setting:-
>
> FFLAGS =3D -std=3Dlegacy -fd-lines-as-code
>
> gets rid of all errors except one. -std=3Dlegacy gets over
> the non
> standard do loop in animate. -fd-lines-as-code gets over
> the objection
> to lines starting with "D" in column 1. That leaves a
> problem with
> format($,' .. in main.f. I just removed the "$,". It the= n
> compiles but
> it does not link. It can not find subroutine filnam. Now I
> am stuck. Any
> thoughts.
>
> This is very old code and it probably only works for G94.
> There was a
> change in format of the coordinates in the output file
> going from G94 to
> G98. I got it from CCL and it is dated "13-Dec-1996 12:00".<= br> > Is there
> anything more recent?
>
> Cheers, Brian.
>
> > To use it, look at the README file included in the the
> source code.
> >
> > Hope this helps,
> > Jason
> >
> > On Sun, Feb 6, 2011 at 8:20 AM, neeraj misra
> neerajmisra++hotmail.= com <
> > owner-chemistry{=3D}= ccl.net> wrote:
> >
> > >
> > > Sent to CCL by: "neeraj=A0 misra"
> [neerajmisra(a)hotmai= l.com]
> > > DEAR MEMBERS,
> > >=A0 =A0 =A0 =A0 =A0 =A0 =A0
> COULD ANYONE TELL ME HOW TO INSTALL GAR2PED PRPGRAM ON
> FEDORA
> > > CORE14..AND HOW TO RUN IT TOO...MY OBJECT IS TO
> CALCULATE THE POTENTIAL
> > > ENERGY DISTRIBUTION..
> > >
> > > THANKS>
> > >
> > >
> > >
> > >
> > > --
> > > Jason M. Swails
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Graduate Student
> > > 352-392-4032
>
> --
> =A0=A0=A0Brian Salter-Duke (Brian Duke)=A0
> Brian.Salter-Duke:mona= sh.edu
> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0
> =A0 =A0=A0=A0Honorary Researcher Fellow
> =A0 =A0 =A0 =A0 =A0 =A0 Monash Institute
> of Pharmaceutical Sciences,
> =A0 =A0 =A0 Monash University Parkville Campus,
> VIC 3052, Australia.
>
>
>
> -=3D This is automatically added to each message by the
> mailing script =3D-
> To recover the email address of the author of the message,
> please change
> the strange characters on the top line to the :: sign. You
> can also>
> E-mail to subscribers: CHEMISTRY::ccl.net
> or use:
> =A0 =A0 =A0>
> E-mail to administrators: CHEMISTRY-REQUE= ST::ccl.net
> or use
> =A0 =A0 =A0> =A0 =A0 =A0> =A0 =A0 =A0>
>
>



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--0016367fb2c7922b96049bacedfe-- From owner-chemistry@ccl.net Mon Feb 7 05:40:01 2011 From: "Simone Kossmann simone]*[thch.uni-bonn.de" To: CCL Subject: CCL: Restarting TDDFT calculation in ORCA 2.8 Message-Id: <-43887-110207053825-16532-djHQ9ISeOlAZ8QJvKJTNnQ . server.ccl.net> X-Original-From: Simone Kossmann Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 07 Feb 2011 11:38:16 +0100 MIME-Version: 1.0 Sent to CCL by: Simone Kossmann [simone(_)thch.uni-bonn.de] Dear David, unfortunately, this is not possible! The MORead feature is the only restart feature, you can make use of. All the best, Simone On 02/04/2011 08:58 PM, David Neil Bowman dnbowman|a|ncsu.edu wrote: > Sent to CCL by: "David Neil Bowman" [dnbowman(0)ncsu.edu] > Is it possible to restart an ORCA TDDFT calculation from where the program halted (time limit restrictions forced this) or from a completed calculation with fewer roots? Currently I have only been able to restart with Guess=MORead and MOInp="myfile.gbw" options from the initial optimization calculation. > > David Bowman > Graduate Student > North Carolina State University, Chemistry Department> From owner-chemistry@ccl.net Mon Feb 7 08:34:00 2011 From: "Wojciech Kolodziejczyk dziecial:-:icnanotox.org" To: CCL Subject: CCL:G: generate electrostatic potential map problem in Gaussian Message-Id: <-43888-110207083211-22753-dy/YMzUo1WZFWld2orMTWA%a%server.ccl.net> X-Original-From: Wojciech Kolodziejczyk Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 7 Feb 2011 14:32:04 +0100 MIME-Version: 1.0 Sent to CCL by: Wojciech Kolodziejczyk [dziecial ~ icnanotox.org] Hi Try tu use cubegen program attached to the gaussian package. I know that Windows GView have some problems with generating ESP. You have to generate cube using cubegen (on the machine in supercomputing center) and then read it into GView in Windows. Otherwise you will meet some problems. W. 2011/2/5 dhacademic dhacademic---gmail.com : > Hi Everyone, > > I experience a problem in generating electrostatic potential map with > Gaussian calculation. I have tried small molecules (2 water molecules). > After single point calculation, the "Total Density" type of cube can be > generated in "GView 3 -- Results -- Surface -- Cube action" with fchk file. > Then with this cube, the "ESP type" new mapped surface can be generated in > "surface action", which is what I expect. > > But for a relative larger system (about 20 atoms), in the "cube action" > step, an error message appears: > "surface build failed. > No data to plot. > Isovalue my be out of range." > > So I tried cubegen to generate potential cube file from fchk file. Then the > following error message appears: > > PGFIO-F-231/formatted read/unit=20/error on data conversion. > File name = 3lbw-DP-DoD1-NMR-fullQM.fchk    formatted, sequential > access   record = 297544 > In source file fchkrd.f, at line number 41 > > I have the following questions: > (1) why the electrostatic potential surface need to be generated based on > "total density" type of cube instead of "ESP" type of cube? I also tried the > latter cube, but a strange surface can be obtained. > > (2) Is there any additional keyword needed in the root section of gaussian > calculation for ESP calculation? > > (3) I do not understand why only ESP of small molecule (< 10 atoms) can be > generated? And why I fail in medium size system? Is there any atom size > limitation for cubegen in both g03 and g09? My friend and I tried both > version, but neither of them can generate potential cube file from fchk > file. The command we used is "cubegen 0 potential a.fchk a_pot.cube 80" > > Any suggestion is appreciated! > > Best, > Hao > From owner-chemistry@ccl.net Mon Feb 7 09:08:00 2011 From: "may abdelghani may01dz-$-yahoo.fr" To: CCL Subject: CCL: NBO5.0 with ADF wave function Message-Id: <-43889-110207075101-4620-FZTTgN0XTxTZiNiJgQRmpg^^server.ccl.net> X-Original-From: may abdelghani Content-Type: multipart/alternative; boundary="0-2103348798-1297083052=:35280" Date: Mon, 7 Feb 2011 12:50:52 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz[a]yahoo.fr] --0-2103348798-1297083052=:35280 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hello, =0A=0A=0A=0A=0A=0AThe NBO Calculations carried out at the DFT-B3LYP/TZP ter= minate normally, whereas thus at LDA/TZP=0Aand BP68/TZP gives these message= errors:=20 FATAL ERROR:=0ATotal number of electrons ( 258.63189) not an integer: =A0Ch= eck input data or density (or try FIXDM=0Akeyword). I try with FIXDM keywor= d but no things happen.....where is the priblem, thanks =0A=0A may abdelghani=09Laboratoire de chimie des mat=E9riaux et des vivants: Acti= vit=E9, R=E9activit=E9 --- En date de=A0: Lun 7.2.11, Simone Kossmann simone]*[thch.uni-bonn.de a =E9crit=A0: De: Simone Kossmann simone]*[thch.uni-bonn.de Objet: CCL: Restarting TDDFT calculation in ORCA 2.8 =C0: "Abdelghani, May " Date: Lundi 7 f=E9vrier 2011, 11h38 Sent to CCL by: Simone Kossmann [simone(_)thch.uni-bonn.de] Dear David, unfortunately, this is not possible! The MORead feature is the only restart= feature, you can make use of. All the best, Simone On 02/04/2011 08:58 PM, David Neil Bowman dnbowman|a|ncsu.edu wrote: > Sent to CCL by: "David Neil Bowman" [dnbowman(0)ncsu.edu] > Is it possible to restart an ORCA TDDFT calculation from where the progra= m halted (time limit restrictions forced this) or from a completed calculat= ion with fewer roots? Currently I have only been able to restart with Guess= =3DMORead and MOInp=3D"myfile.gbw" options from the initial optimization ca= lculation. >=20 > David Bowman > Graduate Student > North Carolina State University, Chemistry Department> -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0=A0=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message=A0 =A0=A0=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message Subscribe/Unsubscribe:=A0 =A0 =A0 http://www.ccl.net/chemistry/sub_unsub.sh= tmlConferences: http://server.ccl.net/chemistry/a= nnouncements/conferences/=A0 =A0=A0=A0http://www.ccl.net/spammers.txt=0A=0A=0A --0-2103348798-1297083052=:35280 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hello,
=0A= =0A=0A=0A

The NBO Calculations carried out at the DFT-B3LYP/TZP terminate norma= lly, whereas thus at LDA/TZP=0Aand BP68/TZP gives these message errors:

FATAL ERROR:=0ATotal number of electrons= ( 258.63189) not an integer:  Check input dat= a or density (or try FIXDM=0Akeyword). I try with FIXDM keyword but no thin= gs happen.....where is the priblem, thanks

=0A=0A









may abdelghani=09
Laboratoire de chimie des mat=E9riaux et des vivants: Act= ivit=E9, R=E9activit=E9


--- En dat= e de : Lun 7.2.11, Simone Kossmann simone]*[thch.uni-bonn.de <= ;owner-chemistry.:.ccl.net> a =E9crit :

De: Simone Kossmann simone]*[thch.uni-bonn.de <owner-chemistry.:.ccl.net><= br>Objet: CCL: Restarting TDDFT calculation in ORCA 2.8
=C0: "Abdelghani= , May " <may01dz.:.yahoo.fr>
Date: Lundi 7 f=E9vrier 2011, 1= 1h38


Sent to CCL by: Simone Kossmann [s= imone(_)thch.uni-bonn.de]
Dear David,

unfortunately, this is not = possible! The MORead feature is the only restart feature, you can make use = of.

All the best,
Simone

On 02/04/2011 08:58 PM, David Nei= l Bowman dnbowman|a|ncsu.edu wrote:
> Sent to CCL by: "David Neil Bow= man" [dnbowman(0)ncsu.edu]
> Is it possible to restart an ORCA TDDFT = calculation from where the program halted (time limit restrictions forced t= his) or from a completed calculation with fewer roots? Currently I have onl= y been able to restart with Guess=3DMORead and MOInp=3D"myfile.gbw" options= from the initial optimization calculation.
>
> David Bowman
> Graduate Student
> North Carolina State University, C= hemistry Department>



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=0A=0A=0A=0A=0A --0-2103348798-1297083052=:35280-- From owner-chemistry@ccl.net Mon Feb 7 11:15:00 2011 From: "angela bruneau amb458..cornell.edu" To: CCL Subject: CCL:G: WebMO user interface: Possible to read checkfiles? Message-Id: <-43890-110207111316-14011-Mn3ln44Y9vcWGnItmc3WoQ a server.ccl.net> X-Original-From: "angela bruneau" Date: Mon, 7 Feb 2011 11:13:14 -0500 Sent to CCL by: "angela bruneau" [amb458##cornell.edu] I have had no success in getting check files read in with WebMO submitting Gaussian calcs. It seems there is a file problem. WebMO seems to create the file that it works in at the time you hit submit; it assigns a directory/job name, and all reads and writes must come from there. You cannot read from other directories (perhaps a Fortran problem) and you cannot specify a directory in lieu of WebMO choosing one. If I am wrong, and there is a way, please let me know. Otherwise I guess people are generally building in GV or Avogadro or something, then just running jobs through command line? I might have to go this route. The thing I like about WebMO is that I can see the energy graph as the job is running so I know quickly if it is oscillating, or if it is generally dropping. What does everyone else do who is not using WebMO? Thanks!! Angela From owner-chemistry@ccl.net Mon Feb 7 12:24:00 2011 From: "Dario Fernando Coral Obando ferchocoralg16]-[gmail.com" To: CCL Subject: CCL:G: IRC defective at low frequencies Message-Id: <-43891-110207100953-31148-5vS6KWq4jxHSy5grIG7/Bg###server.ccl.net> X-Original-From: "Dario Fernando Coral Obando" Date: Mon, 7 Feb 2011 10:09:48 -0500 Sent to CCL by: "Dario Fernando Coral Obando" [ferchocoralg16^_^gmail.com] I work in the modeling of fragmentations of benzoazepines and, I found many conformational changes in the azepine ring. The transition states for these conformational changes usually have low frequencies (between 17 and 50) and for them, i could not get a quality IRC. They have no IRC maximum and only had 3 or at most 4 points, even though more points are specified in the input files. I used the Gaussian 09W package with the following route sections: # irc=(maxpoints=5,calcfc) ub3lyp/6-31g(d) # UB3LYP/6-31G(d) IRC=(CALCFC,MAXPOINTS=40,MAXCYCLE=20) SCF=DIRECT # irc=(maxpoints=10,calcfc,vtight,maxcycle=20,stepsize=1) ub3lyp/6-31+ g(d,p) int=ultrafine scf=direct It would be helpful if you guide me a little about how to calculate these IRC for conformational changes correctly. I'm starting on the topic of computer modeling of reactions and your contributions will be very valuables. Carefully Dario Fernando Coral Obando Chemical student Universidad de Nario, Pasto, Colombia From owner-chemistry@ccl.net Mon Feb 7 13:16:01 2011 From: "Olasunkanmi Lukman Olawale walecomuk*|*yahoo.co.uk" To: CCL Subject: CCL: Organometallic builder Message-Id: <-43892-110207041314-24875-NjyXNhFisoZ4mj4bzaBm8w%a%server.ccl.net> X-Original-From: Olasunkanmi Lukman Olawale Content-Type: multipart/alternative; boundary="0-1874550709-1297069986=:40585" Date: Mon, 7 Feb 2011 09:13:06 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: Olasunkanmi Lukman Olawale [walecomuk(-)yahoo.co.uk] --0-1874550709-1297069986=:40585 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Thanks. I do use Avogadro too. But when it comes to building organometallic= =0Amolecules like Ferrocene in which the connecting bonds between the cent= ral atom =0Aand the ligands are to the aromatic pie electrons and not reall= y atoms, it =0Abecomes a problem using Avogadro. This is my quest. Can anyo= ne then suggest a =0Agood builder that is Windows compatible, works with MO= PAC and could be =0Adownloaded for free?=0A=0A Olasunkanmi Lukman Olawale= =0A________________________________=0ACurrent Address:=0ADepartment of Chem= istry,=0AObafemi Awolowo University,=0AIle-Ife, Osun State.=0ANigeria.=0A= =0A+234-0-80-52401564 Or +234-0-80-67161091=0A_____________________________= ___=0A =0A=0A=0A=0A=0A________________________________=0AFrom: Adam Tenderh= olt atenderholt%a%gmail.com =0ATo: "Olasunkanmi, O= lawale Lukman " =0ASent: Sun, 6 February, 20= 11 23:53:07=0ASubject: CCL: Organometallic builder=0A=0A=0ASent to CCL by: = Adam Tenderholt [atenderholt[A]gmail.com]=0AAvogadro is pretty good at buil= ding molecules. I usually sketch out a=0Astructure and then do a quick MM m= inimization to get a more reasonable=0Astructure.=0A=0A=0AOn Thu, Feb 3, 20= 11 at 2:56 PM, Lukman Olawale Olasunkanmi=0Awaleolasunkanmi/agmail.com wrote:=0A> Dear All,=0A> Does anyone know of a free = molecular builder that is very good at building=0A> organometallic compound= s and it is windows compatible?=0A> Thank you=0A>=0A> --=0A> Olasunkanmi Lu= kman Olawale=0A>=0A> Department of Chemistry,=0A> Obafemi Awolowo Universit= y,=0A> Ile-Ife, Nigeria.=0A> +234-08052401564=0A>=0A> "Improving our own at= titudes and our own state of mind takes time. Haste and=0A> impatience can = only defeat our purposes."=0A>=0A>=0A=0A=0A=0A-=3D This is automatically ad= ded to each message by the mailing script =3D-=0ATo recover the email addre= ss of the author of the message, please change=0Athe strange characters on = the top line to the === sign. You can also=0Alook up the X-Original-From: lin= e in the mail header.=0A=0A= =0A=0A=0AE-mail to adm= inistrators: CHEMISTRY-REQUEST===ccl.net or use=0A http://www.ccl.net/cg= i-bin/ccl/send_ccl_message=0A=0A=0A http://www.= ccl.net/chemistry/sub_unsub.shtml=0A=0ABefore posting, check wait time at: = http://www.ccl.net=0A=0A=0AConferences: http:/= /server.ccl.net/chemistry/announcements/conferences/=0A=0ASearch Messages: = http://www.ccl.net/chemistry/searchccl/index.shtml=0A=0AIf your mail bounce= s from CCL with 5.7.1 error, check:=0A= =0A=0A=0A=0A=0A = --0-1874550709-1297069986=:40585 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Thanks. I do use Avogadro too. But when it comes to building o= rganometallic molecules like Ferrocene in which the connecting bonds betwee= n the central atom and the ligands are to the aromatic pie electrons and no= t really atoms, it becomes a problem using Avogadro. This is my quest. Can = anyone then suggest a good builder that is Windows compatible, works with M= OPAC and  could be downloaded for free?
 
Olasunkanmi Lukman Olawale<= /span>
Current Address:
Department of Chemistry,
Obafemi Awolowo University,
Ile-Ife, Osun State.
Nig= eria.
+234-0-80-52401564 Or +234-0-8= 0-67161091

From: Adam Tenderholt atenderholt%a= %gmail.com <owner-chemistry===ccl.net>
T= o: "Olasunkanmi, Olawale Lukman " <walecomuk===yahoo.co= .uk>
Sent: Sun, 6 Fe= bruary, 2011 23:53:07
Subject: CCL: Organometallic builder


Sent to CCL by: Adam = Tenderholt [atenderholt[A]gmail.com]
Avogadro is pretty good at building= molecules. I usually sketch out a
structure and then do a quick MM mini= mization to get a more reasonable
structure.


On Thu, Feb 3, 2= 011 at 2:56 PM, Lukman Olawale Olasunkanmi
waleolasunkanmi/agmail.com &l= t;owner-chemistry~~ccl.net> wrote:
> Dear All,
> Does anyone= know of a free molecular builder that is very good at building
> org= anometallic compounds and it is windows compatible?
> Thank you
&g= t;
> --
> Olasunkanmi Lukman Olawale
>
> Department of Chemistry,
> Obafemi Awolowo University,
> Ile-I= fe, Nigeria.
> +234-08052401564
>
> "Improving our own at= titudes and our own state of mind takes time. Haste and
> impatience = can only defeat our purposes."
>
>



-=3D This is = automatically added to each message by the mailing script =3D-
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=0A=0A=0A=0A --0-1874550709-1297069986=:40585-- From owner-chemistry@ccl.net Mon Feb 7 13:50:00 2011 From: "sadia zafar diya.khan.05__gmail.com" To: CCL Subject: CCL: problem in running configuration file using NAMD Message-Id: <-43893-110207132654-5692-1hb0PeOuwrac9WfPQxHMPg()server.ccl.net> X-Original-From: sadia zafar Content-Type: multipart/alternative; boundary=0016e6deddc8a2de2c049bb55f1b Date: Mon, 7 Feb 2011 23:26:42 +0500 MIME-Version: 1.0 Sent to CCL by: sadia zafar [diya.khan.05__gmail.com] --0016e6deddc8a2de2c049bb55f1b Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi, Sir your guidance helped me a lot and now I am in a position to understand the differences between every generated file. Can you help me in one more parameter adjustment? I want to ionize my structure as well. How can I measure the concentration of Ca, Mg or K ions to be added? On Sat, Feb 5, 2011 at 8:47 PM, Vincent Leroux vincent.leroux[-]loria.fr < owner-chemistry . ccl.net> wrote: > > Sent to CCL by: Vincent Leroux [vincent.leroux- -loria.fr] > > Hi, > > First of all you should write NAMD configuration files that perform a > single task - this is much easier to understand and maintain. Typically y= ou > start from all-round files minimization.namd, equilibration.namd and > dynamics.namd. > > "Multiple purpose" parameter files ending with an "execution script" phas= e > are IMHO a really bad idea. In addition to visual inspection e.g. with VM= D, > you should check after minimization that there is no red light > >> from the log file, and make sure after equilibration that the system is >> > actually equilibrated (stable energy, pressure, box size etc.). If you do > not do that systematically you might be wasting valuable computational ti= me. > > Then, tuning up the parameters depends on what kind of system you have... > Usually, the better the quality of the starting model, the easier/shorter > the minimization and equilibration. Check scientific publications to see > what others are doing (you will quickly notice there are some conventions= ). > > Here are some sensible starting points - I do not mention parameters > regarding trajectory recording, forcefield, electrostatics, PBC etc., thi= s > is just to highlight the differences between minimization, equilibration = and > dynamics with NAMD. The number of steps correspond to typical values for > simulating medium-sized proteins in explicit solvent. Check the NAMD manu= al > for explanations of the parameters, and description of many alternate > methods. > > > > # minimization.namd > > structure start.psf > coordinates start.pdb > outputName minimized > > fixedAtoms on > fixedAtomsForces on > fixedAtomsCol B # start.pdb B column: 0->free 10->fixed > > minimization on # other related parameters defaults usually ok > numSteps 5000 > > > > # equilibration.namd > # Berendstein's method - temperature assignment/rescaling > > structure start.psf > coordinates start.pdb # not taken into account > binCoordinates minimized.coor # this one instead > extendedSystem minimized.xsc > outputname equilibrated > > berendsenPressure on > berendsenPressureTarget 1.01325 # atmospheric pressure > berendsenPressureCompressibility 4.57e-5 # liquid water > berendsenPressureRelaxationTime 100.0 > berendsenPressureFreq 10 > > temperature 0.5 # starting at 0.5 K > reassignFreq 100 > reassignIncr 0.5 > reassignHold 300 # target T: 300 K > numsteps 100000 # 100 ps, constant T the last 40 ps > > > > # dynamics.namd > # NPT ensemble using Nose-Hoover Langevin piston > > structure start.psf > coordinates start.pdb # not taken into account > binCoordinates equilibrated.coor > binVelocities equilibrated.vel # corresponds to T =3D 300 K > extendedSystem equilibrated.xsc > outputname dyn1-out > > LangevinPiston on > LangevinPistonPeriod 100.0 > LangevinPistonDecay 50.0 > LangevinPistonTarget 1.01325 # constant pressure > LangevinPistonTemp 300 # constant temperature > > numsteps 10000000 # 10 ns MD > > > > Hope it helps. You really have to understand the meaning and purpose of > each single line of your parameter files, or you will have surprises late= r. > If someone just tells you "just copy that standard parameter file > >> from wherever, it will work", don't you think this is too good to be >> > true? ;-) > > Regards > VL > > > > Le 05/02/11 12:16, sadia zafar diya.khan.05 ~~ gmail.com a =E9crit : > >> Hi, >> Thanks for your kind response sir. >> I am using NAMD for the very first time, therefore encountering some >> problems. You are rite. I was told by one of the NAMD users that the >> configuration file with default settings (placed in the NAMD tutorial >> example files) can be used as a standard file without making any change >> in it. >> Can you please guide me that how can i equilibrate my MD? What steps do >> I need to add up in my configuration file for the maintenance of my MD? >> >> On Fri, Feb 4, 2011 at 10:04 PM, Vincent Leroux vincent.lerouxa/loria.fr >> > >> > wrote: >> >> >> Sent to CCL by: Vincent Leroux [vincent.leroux---loria.fr >> ] >> >> Hi, >> >> Look at the bottom of the parameter file. What you have been doing is= : >> - 100 minimization steps >> - assign velocities for 302 K all of a sudden >> - 2500 steps of MD >> >> 100 steps of minimization is probably not enough, but this is not >> the problem. You just go straight from minimization to MD: MD is >> started with a random set of velocities averaged to T =3D 302 K, >> resulting in your system being literally torn apart. The RATTLE >> algorithm tries to compensate for abnormal bond lengths occurring at >> the very first MD step, but of course it fails. >> >> You should do some equilibration after minimization... The comment >> at the beginning of your parameter file is mistaking: it says >> "minimization and equilibration" and below I see the (right) comment >> "do langevin dynamics". Seems like this input file was messed up by >> careless copy-paste operations. >> >> Regards >> VL >> >> >> >> Le 04/02/11 06:59, neha khan diya.khan.05(~)gmail.com >> a =E9crit : >> >> >> Sent to CCL by: "neha khan" [diya.khan.05~~gmail.com >> ] >> >> Respected Sir, >> When i run minimization, the program stopped abnormally. What is >> wrong with my file? >> >> REINITIALIZING VELOCITIES AT STEP 100 TO 302 KELVIN. >> TCL: Running for 2500 steps >> ERROR: Constraint failure in RATTLE algorithm for atom 2775! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 2729! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 1739! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 2926! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 6029! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 2398! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 2202! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 3201! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 5028! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 2390! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 553! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 3136! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 4966! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 1588! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 4118! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 1275! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 771! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 1069! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 4008! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 867! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 919! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 3447! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 6355! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 4747! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 332! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 6837! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 82! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 1542! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 1254! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 9773! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 1193! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 3739! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 9465! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 953! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 10527! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 3678! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 117! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 8745! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 9881! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 10838! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 7839! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 8262! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 9955! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 10206! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 8881! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 10080! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 8404! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 8589! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 8450! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 8308! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 8580! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 8572! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Exiting prematurely; see error messages above. >> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D >> >> WallClock: 74.289345 CPUTime: 74.199997 Memory: 99.713013 MB >> Program finished. >> execve failed to start process "namd2" with status: -1 >> execve failed to start process "namd2" with status: -1 >> execve failed to start process "namd2" with status: -1 >> execve failed to start process "namd2" with status: -1 >> Killed >> >> Below is my configuration file: >> >> >> ############################################################# >> ## JOB DESCRIPTION ## >> ############################################################# >> >> # Minimization and Equilibration of >> # pgl in a Water Sphere >> >> >> ############################################################# >> ## ADJUSTABLE PARAMETERS ## >> ############################################################# >> >> structure ../common/pgl_ws.psf >> coordinates ../common/pgl_ws.pdb >> >> set temperature 302 >> set outputname pgl_ws_eq >> >> firsttimestep 0 >> >> >> ############################################################# >> ## SIMULATION PARAMETERS ## >> ############################################################# >> >> # Input >> paraTypeCharmm on >> parameters ../common/par_all27_prot_lipid.inp >> temperature $temperature >> >> >> # Force-Field Parameters >> exclude scaled1-4 >> 1-4scaling 1.0 >> cutoff 12. >> switching on >> switchdist 10. >> pairlistdist 13.5 >> >> >> # Integrator Parameters >> timestep 2.0 ;# 2fs/step >> rigidBonds all ;# needed for 2fs steps >> nonbondedFreq 1 >> fullElectFrequency 2 >> stepspercycle 10 >> >> >> # Constant Temperature Control >> langevin on ;# do langevin dynamics >> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps >> langevinTemp $temperature >> langevinHydrogen off ;# don't couple langevin bath to >> hydrogens >> >> >> # Output >> outputName $outputname >> >> restartfreq 500 ;# 500steps =3D every 1ps >> dcdfreq 250 >> outputEnergies 100 >> outputPressure 100 >> >> >> ############################################################# >> ## EXTRA PARAMETERS ## >> ############################################################# >> >> # Spherical boundary conditions >> sphericalBC on >> sphericalBCcenter 30.3081743413, 28.8049907121, 15.353994423 >> sphericalBCr1 26.0 >> sphericalBCk1 10 >> sphericalBCexp1 2 >> >> >> ############################################################# >> ## EXECUTION SCRIPT ## >> ############################################################# >> >> # Minimization >> minimize 100 >> reinitvels $temperature >> >> run 2500 ;# 5ps> >> >> >> E-mail to subscribers: CHEMISTRY=3D-=3Dccl.net >> or use:> >> E-mail to administrators: CHEMISTRY-REQUEST=3D-=3Dccl.net >> or useConferences: >> >> http://server.ccl.net/chemistry/announcements/conferences/> >> >> >> > > > -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > --0016e6deddc8a2de2c049bb55f1b Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi,
Sir your guidance helped me a lot and now I am in a position to= understand the differences between every generated file. Can you help me i= n one more parameter adjustment? I want to ionize my structure as well. How= can I measure the concentration of Ca, Mg or K ions to be added?


On Sat, Feb 5, 2011 at 8= :47 PM, Vincent Leroux vincent.leroux[-]loria.f= r <owne= r-chemistry . ccl.net> wrote:

Sent to CCL by: Vincent Leroux [vincent.leroux- -loria.fr]

Hi,

First of all you should write NAMD configuration files that perform a singl= e task - this is much easier to understand and maintain. Typically you star= t from all-round files minimization.namd, equilibration.namd and dynamics.n= amd.

"Multiple purpose" parameter files ending with an "execution= script" phase are IMHO a really bad idea. In addition to visual inspe= ction e.g. with VMD, you should check after minimization that there is no r= ed light
> from the log file, and make sure after equilibration that the system is
actually equilibrated (stable energy, pressure, box size etc.). If you do n= ot do that systematically you might be wasting valuable computational time.=

Then, tuning up the parameters depends on what kind of system you have... U= sually, the better the quality of the starting model, the easier/shorter th= e minimization and equilibration. Check scientific publications to see what= others are doing (you will quickly notice there are some conventions).

Here are some sensible starting points - I do not mention parameters regard= ing trajectory recording, forcefield, electrostatics, PBC etc., this is jus= t to highlight the differences between minimization, equilibration and dyna= mics with NAMD. The number of steps correspond to typical values for simula= ting medium-sized proteins in explicit solvent. Check the NAMD manual for e= xplanations of the parameters, and description of many alternate methods.


# minimization.namd

structure =A0 =A0 =A0 =A0 =A0start.psf
coordinates =A0 =A0 =A0 =A0start.pdb
outputName =A0 =A0 =A0 =A0 minimized

fixedAtoms =A0 =A0 =A0 =A0 on
fixedAtomsForces =A0 on
fixedAtomsCol =A0 =A0 =A0B =A0 =A0 # start.pdb B column: 0->free 10->= fixed

minimization =A0 =A0 =A0 on =A0 =A0# other related parameters defaults usua= lly ok
numSteps =A0 =A0 =A0 =A0 =A0 5000



# equilibration.namd
# Berendstein's method - temperature assignment/rescaling

structure =A0 =A0 =A0 =A0 =A0start.psf
coordinates =A0 =A0 =A0 =A0start.pdb =A0 =A0 =A0 =A0# not taken into accoun= t
binCoordinates =A0 =A0 minimized.coor =A0 # this one instead
extendedSystem =A0 =A0 minimized.xsc
outputname =A0 =A0 =A0 =A0 equilibrated

berendsenPressure =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0on
berendsenPressureTarget =A0 =A0 =A0 =A0 =A0 =A01.01325 =A0 # atmospheric pr= essure
berendsenPressureCompressibility =A0 4.57e-5 =A0 # liquid water
berendsenPressureRelaxationTime =A0 =A0100.0
berendsenPressureFreq =A0 =A0 =A0 =A0 =A0 =A0 =A010

temperature =A0 =A0 =A0 =A0 =A00.5 =A0 =A0 =A0# starting at 0.5 K
reassignFreq =A0 =A0 =A0 =A0 100
reassignIncr =A0 =A0 =A0 =A0 0.5
reassignHold =A0 =A0 =A0 =A0 300 =A0 =A0 =A0# target T: 300 K
numsteps =A0 =A0 =A0 =A0 =A0 =A0 100000 =A0 # 100 ps, constant T the last 4= 0 ps



# dynamics.namd
# NPT ensemble using Nose-Hoover Langevin piston

structure =A0 =A0 =A0 =A0 start.psf
coordinates =A0 =A0 =A0 start.pdb =A0 =A0 =A0 =A0 =A0 # not taken into acco= unt
binCoordinates =A0 =A0equilibrated.coor
binVelocities =A0 =A0 equilibrated.vel =A0 =A0# corresponds to T =3D 300 K<= br> extendedSystem =A0 =A0equilibrated.xsc
outputname =A0 =A0 =A0 =A0dyn1-out

LangevinPiston =A0 =A0 =A0 =A0 on
LangevinPistonPeriod =A0 100.0
LangevinPistonDecay =A0 =A050.0
LangevinPistonTarget =A0 1.01325 =A0 # constant pressure
LangevinPistonTemp =A0 =A0 300 =A0 =A0 =A0 # constant temperature

numsteps =A0 10000000 =A0 # 10 ns MD



Hope it helps. You really have to understand the meaning and purpose of eac= h single line of your parameter files, or you will have surprises later. If= someone just tells you "just copy that standard parameter file
> from wherever, it will work", don't you think this is too good to = be
true? =A0;-)

Regards
VL



Le 05/02/11 12:16, sadia zafar diya.khan.05 ~~ gmail.com a =E9crit :
Hi,
Thanks for your kind response sir.
I am using NAMD for the very first time, therefore encountering some
problems. You are rite. I was told by one of the NAMD users that the
configuration file with default settings (placed in the NAMD tutorial
example files) can be used as a standard file without making any change
in it.
Can you please guide me that how can i equilibrate my MD? What steps do
I need to add up =A0in my configuration file for the maintenance of my MD?<= br>
On Fri, Feb 4, 2011 at 10:04 PM, Vincent Leroux vincent.lerouxa/loria.fr
<http://loria.fr> &= lt;owner-chemistry=3D-=3Dccl.n= et

<mailto:owner-chemi= stry=3D-=3Dccl.net>= > wrote:


=A0 =A0Sent to CCL by: Vincent Leroux [vincent.leroux---loria.fr
=A0 =A0<= http://vincent.leroux---loria.fr>]

=A0 =A0Hi,

=A0 =A0Look at the bottom of the parameter file. What you have been doing = is:
=A0 =A0- 100 minimization steps
=A0 =A0- assign velocities for 302 K all of a sudden
=A0 =A0- 2500 steps of MD

=A0 =A0100 steps of minimization is probably not enough, but this is not =A0 =A0the problem. You just go straight from minimization to MD: MD is =A0 =A0started with a random set of velocities averaged to T =3D 302 K, =A0 =A0resulting in your system being literally torn apart. The RATTLE
=A0 =A0algorithm tries to compensate for abnormal bond lengths occurring a= t
=A0 =A0the very first MD step, but of course it fails.

=A0 =A0You should do some equilibration after minimization... The comment<= br> =A0 =A0at the beginning of your parameter file is mistaking: it says
=A0 =A0"minimization and equilibration" and below I see the (rig= ht) comment
=A0 =A0"do langevin dynamics". Seems like this input file was me= ssed up by
=A0 =A0careless copy-paste operations.

=A0 =A0Regards
=A0 =A0VL



=A0 =A0Le 04/02/11 06:59, neha khan diya.khan.05(~)gmail.com
=A0 =A0<http://gmail.com= > a =E9crit :


=A0 =A0 =A0 =A0Sent to CCL by: "neha =A0khan" [diya.khan.05~~gmail.com
=A0 =A0 =A0 =A0<http://g= mail.com>]

=A0 =A0 =A0 =A0Respected Sir,
=A0 =A0 =A0 =A0When i run minimization, the program stopped abnormally. Wh= at is
=A0 =A0 =A0 =A0wrong with my file?

=A0 =A0 =A0 =A0REINITIALIZING VELOCITIES AT STEP 100 TO 302 KELVIN.
=A0 =A0 =A0 =A0TCL: Running for 2500 steps
=A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 2775= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 2729= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 1739= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 2926= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 6029= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 2398= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 2202= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 3201= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 5028= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 2390= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 553!=
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 3136= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 4966= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 1588= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 4118= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 1275= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 771!=
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 1069= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 4008= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 867!=
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 919!=
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 3447= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 6355= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 4747= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 332!=
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 6837= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 82!<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 1542= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 1254= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 9773= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 1193= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 3739= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 9465= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 953!=
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 1052= 7!
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 3678= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 117!=
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 8745= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 9881= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 1083= 8!
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 7839= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 8262= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 9955= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 1020= 6!
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 8881= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 1008= 0!
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 8404= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 8589= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 8450= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 8308= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 8580= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Constraint failure in RATTLE algorithm for atom 8572= !
=A0 =A0 =A0 =A0ERROR: Constraint failure; simulation has become unstable.<= br> =A0 =A0 =A0 =A0ERROR: Exiting prematurely; see error messages above.
=A0 =A0 =A0 =A0=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D

=A0 =A0 =A0 =A0WallClock: 74.289345 =A0CPUTime: 74.199997 =A0Memory: 99.71= 3013 MB
=A0 =A0 =A0 =A0Program finished.
=A0 =A0 =A0 =A0execve failed to start process "namd2" with statu= s: -1
=A0 =A0 =A0 =A0execve failed to start process "namd2" with statu= s: -1
=A0 =A0 =A0 =A0execve failed to start process "namd2" with statu= s: -1
=A0 =A0 =A0 =A0execve failed to start process "namd2" with statu= s: -1
=A0 =A0 =A0 =A0Killed

=A0 =A0 =A0 =A0Below is my configuration file:


=A0 =A0 =A0 =A0###########################################################= ##
=A0 =A0 =A0 =A0## JOB DESCRIPTION =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 ##
=A0 =A0 =A0 =A0###########################################################= ##

=A0 =A0 =A0 =A0# Minimization and Equilibration of
=A0 =A0 =A0 =A0# pgl in a Water Sphere


=A0 =A0 =A0 =A0###########################################################= ##
=A0 =A0 =A0 =A0## ADJUSTABLE PARAMETERS =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 ##
=A0 =A0 =A0 =A0###########################################################= ##

=A0 =A0 =A0 =A0structure =A0 =A0 =A0 =A0 =A0../common/pgl_ws.psf
=A0 =A0 =A0 =A0coordinates =A0 =A0 =A0 =A0../common/pgl_ws.pdb

=A0 =A0 =A0 =A0set temperature =A0 =A0302
=A0 =A0 =A0 =A0set outputname =A0 =A0 pgl_ws_eq

=A0 =A0 =A0 =A0firsttimestep =A0 =A0 =A00


=A0 =A0 =A0 =A0###########################################################= ##
=A0 =A0 =A0 =A0## SIMULATION PARAMETERS =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 ##
=A0 =A0 =A0 =A0###########################################################= ##

=A0 =A0 =A0 =A0# Input
=A0 =A0 =A0 =A0paraTypeCharmm =A0 =A0 =A0on
=A0 =A0 =A0 =A0parameters =A0 =A0 =A0 =A0 =A0../common/par_all27_prot_lipi= d.inp
=A0 =A0 =A0 =A0temperature =A0 =A0 =A0 =A0 $temperature


=A0 =A0 =A0 =A0# Force-Field Parameters
=A0 =A0 =A0 =A0exclude =A0 =A0 =A0 =A0 =A0 =A0 scaled1-4
=A0 =A0 =A0 =A01-4scaling =A0 =A0 =A0 =A0 =A01.0
=A0 =A0 =A0 =A0cutoff =A0 =A0 =A0 =A0 =A0 =A0 =A012.
=A0 =A0 =A0 =A0switching =A0 =A0 =A0 =A0 =A0 on
=A0 =A0 =A0 =A0switchdist =A0 =A0 =A0 =A0 =A010.
=A0 =A0 =A0 =A0pairlistdist =A0 =A0 =A0 =A013.5


=A0 =A0 =A0 =A0# Integrator Parameters
=A0 =A0 =A0 =A0timestep =A0 =A0 =A0 =A0 =A0 =A02.0 =A0;# 2fs/step
=A0 =A0 =A0 =A0rigidBonds =A0 =A0 =A0 =A0 =A0all =A0;# needed for 2fs step= s
=A0 =A0 =A0 =A0nonbondedFreq =A0 =A0 =A0 1
=A0 =A0 =A0 =A0fullElectFrequency =A02
=A0 =A0 =A0 =A0stepspercycle =A0 =A0 =A0 10


=A0 =A0 =A0 =A0# Constant Temperature Control
=A0 =A0 =A0 =A0langevin =A0 =A0 =A0 =A0 =A0 =A0on =A0 =A0;# do langevin dy= namics
=A0 =A0 =A0 =A0langevinDamping =A0 =A0 5 =A0 =A0 ;# damping coefficient (g= amma) of 5/ps
=A0 =A0 =A0 =A0langevinTemp =A0 =A0 =A0 =A0$temperature
=A0 =A0 =A0 =A0langevinHydrogen =A0 =A0off =A0 =A0;# don't couple lang= evin bath to
=A0 =A0 =A0 =A0hydrogens


=A0 =A0 =A0 =A0# Output
=A0 =A0 =A0 =A0outputName =A0 =A0 =A0 =A0 =A0$outputname

=A0 =A0 =A0 =A0restartfreq =A0 =A0 =A0 =A0 500 =A0 =A0 ;# 500steps =3D eve= ry 1ps
=A0 =A0 =A0 =A0dcdfreq =A0 =A0 =A0 =A0 =A0 =A0 250
=A0 =A0 =A0 =A0outputEnergies =A0 =A0 =A0100
=A0 =A0 =A0 =A0outputPressure =A0 =A0 =A0100


=A0 =A0 =A0 =A0###########################################################= ##
=A0 =A0 =A0 =A0## EXTRA PARAMETERS =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0##
=A0 =A0 =A0 =A0###########################################################= ##

=A0 =A0 =A0 =A0# Spherical boundary conditions
=A0 =A0 =A0 =A0sphericalBC =A0 =A0 =A0 =A0 on
=A0 =A0 =A0 =A0sphericalBCcenter =A0 30.3081743413, 28.8049907121, 15.3539= 94423
=A0 =A0 =A0 =A0sphericalBCr1 =A0 =A0 =A0 26.0
=A0 =A0 =A0 =A0sphericalBCk1 =A0 =A0 =A0 10
=A0 =A0 =A0 =A0sphericalBCexp1 =A0 =A0 2


=A0 =A0 =A0 =A0###########################################################= ##
=A0 =A0 =A0 =A0## EXECUTION SCRIPT =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0##
=A0 =A0 =A0 =A0###########################################################= ##

=A0 =A0 =A0 =A0# Minimization
=A0 =A0 =A0 =A0minimize =A0 =A0 =A0 =A0 =A0 =A0100
=A0 =A0 =A0 =A0reinitvels =A0 =A0 =A0 =A0 =A0$temperature

=A0 =A0 =A0 =A0run 2500 ;# 5ps>


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--0016e6deddc8a2de2c049bb55f1b-- From owner-chemistry@ccl.net Mon Feb 7 14:26:00 2011 From: "Guilherme Luis Cordeiro guilhermecord|*|gmail.com" To: CCL Subject: CCL:G: Optmization error Message-Id: <-43894-110207133244-11105-pa7anqTfydlIpDF1z2N/dA^server.ccl.net> X-Original-From: "Guilherme Luis Cordeiro" Date: Mon, 7 Feb 2011 13:32:42 -0500 Sent to CCL by: "Guilherme Luis Cordeiro" [guilhermecord .. gmail.com] Dear members, could anyone help me solve this optmization problem: Initial guess read from the read-write file: Restarting incremental Fock formation. Restarting incremental Fock formation. Restarting incremental Fock formation. >>>>>>>>>> Convergence criterion not met. SCF Done: E(RHF) = -1097.91175446 A.U. after 65 cycles Convg = 0.2394D-05 -V/T = 2.0014 S**2 = 0.0000 Convergence failure -- run terminated. Error termination via Lnk1e in C:\G98W\l502.exe. My input was as follows: ********************************************* Gaussian 98: x86-Win32-G98RevA.9 19-Apr-2000 06-Feb-2011 ********************************************* %mem=6MW %nproc=1 Will use up to 1 processors via shared memory. %chk=Quercertina.chk Default route: MaxDisk=2000MB --------------------------- #T RHF/6-31+G(d,p) Opt Test --------------------------- ---------------------- Quercetin Optimization ---------------------- Symbolic Z-matrix: Charge = 0 Multiplicity = 1 C C 1 B1 C 2 B2 1 A1 C 3 B3 2 A2 1 D1 0 O 4 B4 3 A3 2 D2 0 C 5 B5 4 A4 3 D3 0 O 3 B6 2 A5 1 D4 0 O 1 B7 2 A6 3 D5 0 O 2 B8 1 A7 6 D6 0 C 3 B9 2 A8 1 D7 0 C 4 B10 3 A9 2 D8 0 C 11 B11 4 A10 3 D9 0 C 10 B12 3 A11 2 D10 0 H 11 B13 4 A12 3 D11 0 O 12 B14 11 A13 4 D12 0 H 13 B15 10 A14 3 D13 0 C 6 B16 5 A15 4 D14 0 C 17 B17 6 A16 5 D15 0 C 18 B18 17 A17 6 D16 0 C 19 B19 18 A18 17 D17 0 C 20 B20 19 A19 18 D18 0 C 17 B21 6 A20 5 D19 0 H 18 B22 17 A21 6 D20 0 O 19 B23 18 A22 17 D21 0 O 20 B24 19 A23 18 D22 0 H 21 B25 20 A24 19 D23 0 H 22 B26 17 A25 6 D24 0 H 12 B27 11 A26 4 D25 0 H 3 B28 2 A27 1 D26 0 H 1 B29 2 A28 3 D27 0 H 19 B30 18 A29 17 D28 0 H 20 B31 19 A30 18 D29 0 Variables: B1 1.3728 B2 1.42201 B3 1.41887 B4 1.42172 B5 1.37334 B6 2.45285 B7 1.43 B8 1.43 B9 1.42203 B10 1.42208 B11 1.37286 B12 1.37294 B13 1.10035 B14 1.43 B15 1.09995 B16 1.54 B17 1.39516 B18 1.39471 B19 1.39543 B20 1.39483 B21 1.39483 B22 1.09966 B23 1.43 B24 1.43 B25 1.09976 B26 1.0996 B27 1.9702 B28 3.24788 B29 1.9702 B30 1.9702 B31 1.9702 A1 120.50995 A2 119.0959 A3 119.21033 A4 120.45591 A5 90.92589 A6 120.64768 A7 120.8832 A8 121.70036 A9 119.05963 A10 120.54905 A11 120.49677 A12 118.59132 A13 120.64917 A14 120.68504 A15 120.64565 A16 119.99722 A17 120.00863 A18 119.99417 A19 119.99399 A20 120.00432 A21 119.98077 A22 120.0128 A23 119.98114 A24 120.01134 A25 120.008 A26 147.99709 A27 101.86544 A28 93.29976 A29 92.66488 A30 92.63322 D1 0.0171 D2 -0.00956 D3 -0.00404 D4 -179.99446 D5 179.99516 D6 -179.99714 D7 -179.98755 D8 179.99469 D9 0.00145 D10 -179.99953 D11 179.99838 D12 179.98387 D13 179.99873 D14 -179.99903 D15 0.03597 D16 -179.97293 D17 -0.05684 D18 0.03411 D19 -179.9693 D20 -0.05203 D21 179.96185 D22 -179.99644 D23 -179.99951 D24 -0.00555 D25 179.99535 D26 -179.99566 D27 179.99516 D28 179.94629 D29 -179.99835 Thanks. From owner-chemistry@ccl.net Mon Feb 7 15:00:01 2011 From: "Olasunkanmi Lukman Olawale walecomuk(a)yahoo.co.uk" To: CCL Subject: CCL: dissenting results Message-Id: <-43895-110207135818-11061-/kQqxWRPtXBwAsOfnTCXPg#%#server.ccl.net> X-Original-From: Olasunkanmi Lukman Olawale Content-Type: multipart/alternative; boundary="0-536457798-1297105087=:45503" Date: Mon, 7 Feb 2011 18:58:07 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: Olasunkanmi Lukman Olawale [walecomuk[]yahoo.co.uk] --0-536457798-1297105087=:45503 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Thank you Victor. I got your explanation but something still baffles me.=0A= If I run the MOPAC job without the THERMO key word I will get some paramete= rs: =0Ae.g. final heat of formation, total energy, electronic energy etc. = =0A=0ABut, with THERMO key word, most often I experience this kind of warni= ng/error:=0A** GRADIENT IS TOO LARGE TO ALLOW FORCE MATRIX TO BE CALCULATED= , (LIMIT=3D10) **=0A EITHER ADD 'LET' OR REDUCE GRADIENT=0A USING 'TS' OR O= THER GEOMETRY OPTIMIZER=0A=0AIt will however give a value for the heat of f= ormation again, this time around =0Asomehow different from the former value= . A typical case for 1,10-phenanthroline:=0A FINAL HEAT OF FORMATION =3D = 81.10951 KCAL/MOL =3D 339.36220 KJ/MOL=0Awithout using the THERMO keyword.= =0A=0AAND=0A=0AHEAT OF FORMATION =3D 89.398345 KCALS/MOLE=0Awhen the T= HERMO keyword was used.=0ASo what do you suggest I do?=0A=0A Olasunkanmi Lu= kman Olawale=0A________________________________=0ACurrent Address:=0ADepart= ment of Chemistry,=0AObafemi Awolowo University,=0AIle-Ife, Osun State.=0AN= igeria.=0A=0A+234-0-80-52401564 Or +234-0-80-67161091=0A___________________= _____________=0A =0A=0A=0A=0A=0A________________________________=0AFrom: Vi= ctor Rosas Garcia rosas.victor*gmail.com =0ATo: "O= lasunkanmi, Olawale Lukman " =0ASent: Fri, 4= February, 2011 13:53:11=0ASubject: CCL: dissenting results=0A=0AGNORM =3D = 109.40376?=0A =0AThat is *huge*. How did you get such a specific number, b= y the way?=0A=0AAnyway, you should be careful with the use of LET. From th= e manual =0A(http://www.openmopac.net/manual/index.html):=0A=0A Now LET = means essentially "I know what I'm doing, override safety checks".=0A Cu= rrently, LET has the following meanings:=0A 1.In a FORCE calculation, it= means that the supplied geometry is to be used, =0Aeven if the gradients a= re large.So you are giving MOPAC a geometry that is not =0Aconverged, and t= elling it to do THERMO no matter what. You could try doing the =0Aoptimiza= tion using PRECISE and then do the FORCE calc without LET and GNORM.=0A=0AT= he manual is your friend! =0A=0AHope this helps and have a nice day=0A=0AVi= ctor=0A=0A2011/2/3 Lukman Olawale Olasunkanmi waleolasunkanmi=3D=3D=3Dgmail= .com =0A=0A=0AThank you.=0A>Here are typical resu= lts:=0A>After geometry optimization without any special keyword:=0A>FINAL H= EAT OF FORMATION =3D 40.08240 KCAL/MOL =0A>=0A>With keyword "thermo", and = LET GNORM =3D 109.40376=0A>=0A>HEAT OF FORMATION =3D 43.366029 KCALS/M= OLE=0A>=0A>Sometimes the difference may be up to 10kcal/mol for some calcul= ations. =0A>Kindly give me an advice on it.=0A>thanks.=0A>=0A>=0A>wrote:=0A= >=0A>=0A>>Sent to CCL by: "Close, David M." [CLOSED!A!mail.etsu.edu]=0A>>Th= is is very interesting. But you need to tell us how much the numbers diffe= r. =0A>> I can see how sometimes very small difference could arise from cod= ing errors =0A>>arising from one subroutine using a double precision variab= le, and another =0A>>subroutine using the same variable with a different wo= rd-length. But these =0A>>would be very small differences. Give us an exa= mple of how big the differences =0A>>are, and what keywords are used to con= trol the accuracy of each SCF cycle.=0A>> Regards, Dave Close.=0A>>=0A>>---= --Original Message-----=0A>>> From: owner-chemistry+closed=3D=3Detsu.edu-$-= ccl.net =0A>>>[mailto:owner-chemistry+closed=3D=3Detsu.edu-$-ccl.net] On Be= half Of Lukman Olawale =0A>>>Olasunkanm waleolasunkanmi:gmail.com=0A>>Sent:= Tuesday, February 01, 2011 8:43 AM=0A>>To: Close, David M.=0A>>Subject: CC= L: dissenting results=0A>>=0A>>=0A>>Sent to CCL by: "Lukman Olawale Olasunk= anm" [waleolasunkanmi#,#gmail.com]=0A>>Hello everyone,=0A>>I usually run my= MOPAC job twice: first for ordinary optimization from which I =0A>>normall= y get the GNORM value ( and H.O.F., dipole moments, HOMO-LUMO, COSMOS =0A>>= Area and volume etc.), and second for the thermo values (with the specified= =0A>>value of the GNORM using the LET keyword). I discovered that the valu= es got for =0A>>the common parameters like H.O.F, dipole moments etc. in bo= th cases differ.=0A>>What can you advise me to do please?=0A>>Thank =0A>>yo= uhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistr= y/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt=0A>>=0A>>=0A>>=0A>>-=3D Th= is is automatically added to each message by the mailing script =3D- =0A>>E= -mail to subscribers: CHEMISTRY-x-ccl.net or use:=0A>> http://www.ccl.n= et/cgi-bin/ccl/send_ccl_message=0A>>=0A>>E-mail to administrators: CHEMISTR= Y-REQUEST-x-ccl.net or use=0A>> http://www.ccl.net/cgi-bin/ccl/send_ccl= _message=0A>>=0A>>Subscribe/Unsubscribe:=0A>> http://www.ccl.net/chemis= try/sub_unsub.shtml=0A>>=0A>>Before posting, check wait time at: http://www= .ccl.net=0A>>=0A>>Job: http://www.ccl.net/jobs=0A>>Conferences: http://serv= er.ccl.net/chemistry/announcements/conferences/=0A>>=0A>>Search Messages: h= ttp://www.ccl.net/chemistry/searchccl/index.shtml=0A>> http://www.ccl.n= et/spammers.txt=0A>>=0A>>RTFI: http://www.ccl.net/chemistry/aboutccl/instru= ctions/=0A>>=0A>>=0A>>=0A>=0A>=0A>-- =0A>Olasunkanmi Lukman Olawale=0A>=0A>= Department of Chemistry,=0A>Obafemi Awolowo University,=0A>Ile-Ife, Nigeria= .=0A>+234-08052401564=0A>=0A>"Improving our own attitudes and our own state= of mind takes time. Haste and =0A>impatience can only defeat our purposes.= "=0A>=0A>=0A=0A=0A=0A --0-536457798-1297105087=:45503 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Thank you Victor. I got your explanation but something still b= affles me.
If I run the MOPAC job without the THERMO key word I will get= some parameters: e.g. final heat of formation, total energy, electronic en= ergy etc.
But, with THERMO key word, most often I experience this kind = of warning/error:
** GRADIENT IS TOO LARGE TO ALLOW FORCE MATRIX TO BE C= ALCULATED, (LIMIT=3D10) **
 EITHER ADD 'LET' OR REDUCE GRADIENT
=  USING 'TS' OR OTHER GEOMETRY OPTIMIZER

It will however give a = value for the heat of formation again, this time around somehow different f= rom the former value. A typical case for 1,10-phenanthroline:
 FINA= L HEAT OF FORMATION =3D   81.10951 KCAL/MOL =3D 339.36220 KJ/MOL<= br>without using the THERMO keyword.

AND

HEAT OF FORMATION =3D      89.398345 KCALS/MOLE
when the THERMO = keyword was used.
So what do you suggest I do?

 Olasunkanmi Lukman Olawale
Current Address:
Department of Chemistry,
Obafemi Awolowo University,
Ile-Ife, Osun State.
Nigeria.
<= div style=3D"text-align: left;">+234-0-80-52401564 Or +234-0-8= 0-67161091

From: Victor Rosas Garcia= rosas.victor*gmail.com <owner-chemistry a ccl.net>
To: "Olasunkanmi, Olawale Lukman -id#43q= -" <walecomuk a yahoo.co.uk>
S= ent: Fri, 4 February, 2011 13:53:11
Subject: CCL: dissenting results

GNORM =3D 109.40376= ?
 
That is *huge*.  How did you get such a specific number, by the way?

A= nyway, you should be careful with the use of LET.  From the manual (http://www.openmopac.net/manual/index.html):
=0A

&nbs= p;   Now LET means essentially "I know what I'm doing, o= verride safety checks".

=0A

    Currently, LET= has the following meanings:

=0A
    1.In a FORCE calculation, it means that the supplied geometr= y is to be used, even if the gradients are large.
So you are givin= g MOPAC a geometry that is not converged, and telling it to do THERMO no ma= tter what.  You could try doing the optimization using PRECISE and the= n do the FORCE calc without LET and GNORM.
=0A
The manual is your fri= end!

Hope this helps and have a nice day

Victor

2011/= 2/3 Lukman Olawale Olasunkanmi waleolasunkanmi=3D=3D=3Dgmail.com <owner-chemistry**ccl.n= et>
=0A
Thank you.
Here are typical results:After geometry optimization without any special keyword:
=0AFINAL HEAT= OF FORMATION =3D  40.08240 KCAL/MOL

With keyword "thermo", an= d LET GNORM =3D 109.40376

=0AHEAT OF FORMATION =3D   =    43.366029 KCALS/MOLE

Sometimes the difference may be up= to 10kcal/mol for some calculations.
Kindly give me an advice on it.thanks.


wrote:
=0A=0A
=0ASent to CCL by: "Clos= e, David M." [CLOSED!A!mail.etsu.edu]
=0AThis is very interesting.  Bu= t you need to tell us how much the numbers differ.  I can see how some= times very small difference could arise from coding errors arising from one= subroutine using a double precision variable, and another subroutine using= the same variable with a different word-length.  But these would be v= ery small differences.  Give us an example of how big the differences = are, and what keywords are used to control the accuracy of each SCF cycle.<= br>=0A=0A=0A  Regards, Dave Close.
=0A
=0A-----Original Message-= ----
=0A> From: owner-chemistry+closed=3D=3Detsu.edu-$-ccl.net [mailto:owner-chemistry+closed=3D=3De= tsu.edu-$-ccl= .net] On Behalf Of Lukman Olawale Olasunkanm waleolasunkanmi:gmail.com
=0A= =0A=0ASent: Tuesday, February 01, 2011 8:43 AM
=0ATo: Close, David M.=0ASubject: CCL: dissenting results
=0A
=0A
=0ASent to CCL by: "L= ukman Olawale Olasunkanm" [waleolasunkanmi#,#gmail.com]
=0AHello everyone,
= =0AI usually run my MOPAC job twice: first for ordinary optimization from w= hich I normally get the GNORM value ( and H.O.F., dipole moments, HOMO-LUMO= , COSMOS Area and volume etc.), and second for the thermo values (with the = specified value of the GNORM using the LET keyword). I discovered that the = values got for the common parameters like H.O.F, dipole moments etc. in bot= h cases differ.
=0A=0A=0AWhat can you advise me to do please?
=0AThan= k youhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehtt= p://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt
=0A=0A=0A
=0A
=0A-=3D This is automatically added to each messag= e by the mailing script =3D-=0A
=0AE-mail to subscribers: CHEMISTRY-x-ccl.net or use:
=0A    = ;  http://www.ccl.net/cgi-bin/ccl/send_ccl_message=
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=0AE-mail to administrators: CHEMISTRY-REQUEST-x-ccl.net or use
=0A  =    http://www.ccl.net/cgi-bin/ccl/send_ccl_m= essage
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= =0ABefore posting, check wait time at: http://www.ccl.net
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=0AJob: http://w= ww.ccl.net/jobs
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=0ARTFI: http://www.ccl.net/ch= emistry/aboutccl/instructions/
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<= br>

--
Olasunkanmi Lukman Olawale

Department of Chemistry,=
Obafemi Awolowo University,
=0A=0AIle-Ife, Nigeria.=
+234-08052401564

"Improving our own attitudes and our own state = of mind takes time. Haste and impatience can only defeat our purposes."=
=0A=0A
=0A

=0A
=0A
=0A=0A=0A=0A = --0-536457798-1297105087=:45503-- From owner-chemistry@ccl.net Mon Feb 7 16:01:00 2011 From: "eurisco1- -pochta.ru" To: CCL Subject: CCL:G: Optmization error Message-Id: <-43896-110207155953-26843-R8K9N5rHGN6PotM3Y4j8wA[*]server.ccl.net> X-Original-From: Content-Transfer-Encoding: 8bit Content-Type: text/plain; format=flowed; charset="koi8-r"; reply-type=original Date: Mon, 7 Feb 2011 23:59:10 +0300 MIME-Version: 1.0 Sent to CCL by: [eurisco1=pochta.ru] Dear Guilherme Luis Cordeiro, I would suggest to modify the route card #T RHF/6-31+G(d,p) Opt Test to # RHF/6-31+G(d,p) Opt(gdiis,maxcycle=100) scf(xqc,vshift=150,maxcycle=512) Sincerely, Ol Ga -----éÓÈÏÄÎÏÅ ÓÏÏÂÝÅÎÉÅ----- > From: Guilherme Luis Cordeiro guilhermecord|*|gmail.com Sent: Monday, February 07, 2011 9:32 PM To: Ga, Ol Subject: CCL:G: Optmization error Sent to CCL by: "Guilherme Luis Cordeiro" [guilhermecord .. gmail.com] Dear members, could anyone help me solve this optmization problem: Initial guess read from the read-write file: Restarting incremental Fock formation. Restarting incremental Fock formation. Restarting incremental Fock formation. >>>>>>>>>> Convergence criterion not met. SCF Done: E(RHF) = -1097.91175446 A.U. after 65 cycles Convg = 0.2394D-05 -V/T = 2.0014 S**2 = 0.0000 Convergence failure -- run terminated. Error termination via Lnk1e in C:\G98W\l502.exe. My input was as follows: ********************************************* Gaussian 98: x86-Win32-G98RevA.9 19-Apr-2000 06-Feb-2011 ********************************************* %mem=6MW %nproc=1 Will use up to 1 processors via shared memory. %chk=Quercertina.chk Default route: MaxDisk=2000MB --------------------------- #T RHF/6-31+G(d,p) Opt Test --------------------------- ---------------------- Quercetin Optimization ---------------------- Symbolic Z-matrix: Charge = 0 Multiplicity = 1 C C 1 B1 C 2 B2 1 A1 C 3 B3 2 A2 1 D1 0 O 4 B4 3 A3 2 D2 0 C 5 B5 4 A4 3 D3 0 O 3 B6 2 A5 1 D4 0 O 1 B7 2 A6 3 D5 0 O 2 B8 1 A7 6 D6 0 C 3 B9 2 A8 1 D7 0 C 4 B10 3 A9 2 D8 0 C 11 B11 4 A10 3 D9 0 C 10 B12 3 A11 2 D10 0 H 11 B13 4 A12 3 D11 0 O 12 B14 11 A13 4 D12 0 H 13 B15 10 A14 3 D13 0 C 6 B16 5 A15 4 D14 0 C 17 B17 6 A16 5 D15 0 C 18 B18 17 A17 6 D16 0 C 19 B19 18 A18 17 D17 0 C 20 B20 19 A19 18 D18 0 C 17 B21 6 A20 5 D19 0 H 18 B22 17 A21 6 D20 0 O 19 B23 18 A22 17 D21 0 O 20 B24 19 A23 18 D22 0 H 21 B25 20 A24 19 D23 0 H 22 B26 17 A25 6 D24 0 H 12 B27 11 A26 4 D25 0 H 3 B28 2 A27 1 D26 0 H 1 B29 2 A28 3 D27 0 H 19 B30 18 A29 17 D28 0 H 20 B31 19 A30 18 D29 0 Variables: B1 1.3728 B2 1.42201 B3 1.41887 B4 1.42172 B5 1.37334 B6 2.45285 B7 1.43 B8 1.43 B9 1.42203 B10 1.42208 B11 1.37286 B12 1.37294 B13 1.10035 B14 1.43 B15 1.09995 B16 1.54 B17 1.39516 B18 1.39471 B19 1.39543 B20 1.39483 B21 1.39483 B22 1.09966 B23 1.43 B24 1.43 B25 1.09976 B26 1.0996 B27 1.9702 B28 3.24788 B29 1.9702 B30 1.9702 B31 1.9702 A1 120.50995 A2 119.0959 A3 119.21033 A4 120.45591 A5 90.92589 A6 120.64768 A7 120.8832 A8 121.70036 A9 119.05963 A10 120.54905 A11 120.49677 A12 118.59132 A13 120.64917 A14 120.68504 A15 120.64565 A16 119.99722 A17 120.00863 A18 119.99417 A19 119.99399 A20 120.00432 A21 119.98077 A22 120.0128 A23 119.98114 A24 120.01134 A25 120.008 A26 147.99709 A27 101.86544 A28 93.29976 A29 92.66488 A30 92.63322 D1 0.0171 D2 -0.00956 D3 -0.00404 D4 -179.99446 D5 179.99516 D6 -179.99714 D7 -179.98755 D8 179.99469 D9 0.00145 D10 -179.99953 D11 179.99838 D12 179.98387 D13 179.99873 D14 -179.99903 D15 0.03597 D16 -179.97293 D17 -0.05684 D18 0.03411 D19 -179.9693 D20 -0.05203 D21 179.96185 D22 -179.99644 D23 -179.99951 D24 -0.00555 D25 179.99535 D26 -179.99566 D27 179.99516 D28 179.94629 D29 -179.99835 Thanks.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Feb 7 16:36:00 2011 From: "eurisco1**pochta.ru" To: CCL Subject: CCL:G: IRC defective at low frequencies Message-Id: <-43897-110207161557-8324-j8ppfD0XmOM3I47Sop+tSQ{}server.ccl.net> X-Original-From: Content-Transfer-Encoding: 8bit Content-Type: text/plain; format=flowed; charset="koi8-r"; reply-type=original Date: Tue, 8 Feb 2011 00:15:16 +0300 MIME-Version: 1.0 Sent to CCL by: [eurisco1-.-pochta.ru] Dear Dario Fernando Coral Obando, Transition states which you have found are particularly loose. I would think that TIGHT option was set in Opt . For IRC calculation in this difficult case I would suggest to add IOP(1/7=100) or IOP(1/7=50) and modify your IRC to IRC(CalcAll,other_options). I hope it will help. Sincerely, Ol Ga -----éÓÈÏÄÎÏÅ ÓÏÏÂÝÅÎÉÅ----- > From: Dario Fernando Coral Obando ferchocoralg16]-[gmail.com Sent: Monday, February 07, 2011 6:09 PM To: Ga, Ol Subject: CCL:G: IRC defective at low frequencies Sent to CCL by: "Dario Fernando Coral Obando" [ferchocoralg16^_^gmail.com] I work in the modeling of fragmentations of benzoazepines and, I found many conformational changes in the azepine ring. The transition states for these conformational changes usually have low frequencies (between 17 and 50) and for them, i could not get a quality IRC. They have no IRC maximum and only had 3 or at most 4 points, even though more points are specified in the input files. I used the Gaussian 09W package with the following route sections: # irc=(maxpoints=5,calcfc) ub3lyp/6-31g(d) # UB3LYP/6-31G(d) IRC=(CALCFC,MAXPOINTS=40,MAXCYCLE=20) SCF=DIRECT # irc=(maxpoints=10,calcfc,vtight,maxcycle=20,stepsize=1) ub3lyp/6-31+ g(d,p) int=ultrafine scf=direct It would be helpful if you guide me a little about how to calculate these IRC for conformational changes correctly. I'm starting on the topic of computer modeling of reactions and your contributions will be very valuables. Carefully Dario Fernando Coral Obando Chemical student Universidad de Nario, Pasto, Colombiahttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Feb 7 17:10:00 2011 From: "Vincent Leroux vincent.leroux+/-loria.fr" To: CCL Subject: CCL: problem in running configuration file using NAMD Message-Id: <-43898-110207164924-19106-h+TnD3WRrbpdh+WzOxFlOA!A!server.ccl.net> X-Original-From: Vincent Leroux Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 07 Feb 2011 22:49:10 +0100 MIME-Version: 1.0 Sent to CCL by: Vincent Leroux [vincent.leroux|*|loria.fr] Hi, Spotting the differences between these input files is not enough: you really need to know the meaning of each single line, what terms like "Langevin piston" exactly stands for from a thermodynamics point of view... You will not go far if you are just being told what to do. You need to understand the concepts in depth, the "trial-and-error" approach is a dead-end if you only count on it. I just provided you with some examples, the context of those might not be optimal for the system you want to model: some other approaches supported by NAMD might be better suited. Regarding the ionization, it is not clear what you want to do. It certainly relates to modeling: it is not the purpose of NAMD, a molecular mechanics program you use on systems that are modeled already. Regards, VL Le 07/02/11 19:26, sadia zafar diya.khan.05__gmail.com a écrit : > > Hi, > Sir your guidance helped me a lot and now I am in a position to > understand the differences between every generated file. Can you help me > in one more parameter adjustment? I want to ionize my structure as well. > How can I measure the concentration of Ca, Mg or K ions to be added? > > > On Sat, Feb 5, 2011 at 8:47 PM, Vincent Leroux vincent.leroux[-]loria.fr > > wrote: > > > Sent to CCL by: Vincent Leroux [vincent.leroux- -loria.fr > ] > > Hi, > > First of all you should write NAMD configuration files that perform > a single task - this is much easier to understand and maintain. > Typically you start from all-round files minimization.namd, > equilibration.namd and dynamics.namd. > > "Multiple purpose" parameter files ending with an "execution script" > phase are IMHO a really bad idea. In addition to visual inspection > e.g. with VMD, you should check after minimization that there is no > red light > > > from the log file, and make sure after equilibration that the > system is > > actually equilibrated (stable energy, pressure, box size etc.). If > you do not do that systematically you might be wasting valuable > computational time. > > Then, tuning up the parameters depends on what kind of system you > have... Usually, the better the quality of the starting model, the > easier/shorter the minimization and equilibration. Check scientific > publications to see what others are doing (you will quickly notice > there are some conventions). > > Here are some sensible starting points - I do not mention parameters > regarding trajectory recording, forcefield, electrostatics, PBC > etc., this is just to highlight the differences between > minimization, equilibration and dynamics with NAMD. The number of > steps correspond to typical values for simulating medium-sized > proteins in explicit solvent. Check the NAMD manual for explanations > of the parameters, and description of many alternate methods. > > > > # minimization.namd > > structure start.psf > coordinates start.pdb > outputName minimized > > fixedAtoms on > fixedAtomsForces on > fixedAtomsCol B # start.pdb B column: 0->free 10->fixed > > minimization on # other related parameters defaults usually ok > numSteps 5000 > > > > # equilibration.namd > # Berendstein's method - temperature assignment/rescaling > > structure start.psf > coordinates start.pdb # not taken into account > binCoordinates minimized.coor # this one instead > extendedSystem minimized.xsc > outputname equilibrated > > berendsenPressure on > berendsenPressureTarget 1.01325 # atmospheric pressure > berendsenPressureCompressibility 4.57e-5 # liquid water > berendsenPressureRelaxationTime 100.0 > berendsenPressureFreq 10 > > temperature 0.5 # starting at 0.5 K > reassignFreq 100 > reassignIncr 0.5 > reassignHold 300 # target T: 300 K > numsteps 100000 # 100 ps, constant T the last 40 ps > > > > # dynamics.namd > # NPT ensemble using Nose-Hoover Langevin piston > > structure start.psf > coordinates start.pdb # not taken into account > binCoordinates equilibrated.coor > binVelocities equilibrated.vel # corresponds to T = 300 K > extendedSystem equilibrated.xsc > outputname dyn1-out > > LangevinPiston on > LangevinPistonPeriod 100.0 > LangevinPistonDecay 50.0 > LangevinPistonTarget 1.01325 # constant pressure > LangevinPistonTemp 300 # constant temperature > > numsteps 10000000 # 10 ns MD > > > > Hope it helps. You really have to understand the meaning and purpose > of each single line of your parameter files, or you will have > surprises later. If someone just tells you "just copy that standard > parameter file > > > from wherever, it will work", don't you think this is too > good to be > > true? ;-) > > Regards > VL > > > > Le 05/02/11 12:16, sadia zafar diya.khan.05 ~~ gmail.com > a écrit : > > Hi, > Thanks for your kind response sir. > I am using NAMD for the very first time, therefore encountering some > problems. You are rite. I was told by one of the NAMD users that the > configuration file with default settings (placed in the NAMD > tutorial > example files) can be used as a standard file without making any > change > in it. > Can you please guide me that how can i equilibrate my MD? What > steps do > I need to add up in my configuration file for the maintenance > of my MD? > > On Fri, Feb 4, 2011 at 10:04 PM, Vincent Leroux > vincent.lerouxa/loria.fr > > > =-=ccl.net > >> wrote: > > > Sent to CCL by: Vincent Leroux [vincent.leroux---loria.fr > > ] > > Hi, > > Look at the bottom of the parameter file. What you have been > doing is: > - 100 minimization steps > - assign velocities for 302 K all of a sudden > - 2500 steps of MD > > 100 steps of minimization is probably not enough, but this > is not > the problem. You just go straight from minimization to MD: MD is > started with a random set of velocities averaged to T = 302 K, > resulting in your system being literally torn apart. The RATTLE > algorithm tries to compensate for abnormal bond lengths > occurring at > the very first MD step, but of course it fails. > > You should do some equilibration after minimization... The > comment > at the beginning of your parameter file is mistaking: it says > "minimization and equilibration" and below I see the (right) comment > "do langevin dynamics". Seems like this input file was messed up by > careless copy-paste operations. > > Regards > VL > > > > Le 04/02/11 06:59, neha khan diya.khan.05(~)gmail.com > > a écrit : > > > Sent to CCL by: "neha khan" [diya.khan.05~~gmail.com > > ] > > Respected Sir, > When i run minimization, the program stopped abnormally. > What is > wrong with my file? > > REINITIALIZING VELOCITIES AT STEP 100 TO 302 KELVIN. > TCL: Running for 2500 steps > ERROR: Constraint failure in RATTLE algorithm for atom 2775! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 2729! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 1739! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 2926! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 6029! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 2398! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 2202! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 3201! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 5028! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 2390! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 553! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 3136! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 4966! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 1588! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 4118! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 1275! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 771! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 1069! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 4008! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 867! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 919! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 3447! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 6355! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 4747! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 332! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 6837! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 82! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 1542! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 1254! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 9773! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 1193! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 3739! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 9465! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 953! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom > 10527! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 3678! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 117! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8745! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 9881! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom > 10838! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 7839! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8262! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 9955! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom > 10206! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8881! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom > 10080! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8404! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8589! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8450! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8308! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8580! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8572! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Exiting prematurely; see error messages above. > ==================================================== > > WallClock: 74.289345 CPUTime: 74.199997 Memory: > 99.713013 MB > Program finished. > execve failed to start process "namd2" with status: -1 > execve failed to start process "namd2" with status: -1 > execve failed to start process "namd2" with status: -1 > execve failed to start process "namd2" with status: -1 > Killed > > Below is my configuration file: > > > > ############################################################# > ## JOB DESCRIPTION > ## > > ############################################################# > > # Minimization and Equilibration of > # pgl in a Water Sphere > > > > ############################################################# > ## ADJUSTABLE PARAMETERS > ## > > ############################################################# > > structure ../common/pgl_ws.psf > coordinates ../common/pgl_ws.pdb > > set temperature 302 > set outputname pgl_ws_eq > > firsttimestep 0 > > > > ############################################################# > ## SIMULATION PARAMETERS > ## > > ############################################################# > > # Input > paraTypeCharmm on > parameters ../common/par_all27_prot_lipid.inp > temperature $temperature > > > # Force-Field Parameters > exclude scaled1-4 > 1-4scaling 1.0 > cutoff 12. > switching on > switchdist 10. > pairlistdist 13.5 > > > # Integrator Parameters > timestep 2.0 ;# 2fs/step > rigidBonds all ;# needed for 2fs steps > nonbondedFreq 1 > fullElectFrequency 2 > stepspercycle 10 > > > # Constant Temperature Control > langevin on ;# do langevin dynamics > langevinDamping 5 ;# damping coefficient (gamma) > of 5/ps > langevinTemp $temperature > langevinHydrogen off ;# don't couple langevin bath to > hydrogens > > > # Output > outputName $outputname > > restartfreq 500 ;# 500steps = every 1ps > dcdfreq 250 > outputEnergies 100 > outputPressure 100 > > > > ############################################################# > ## EXTRA PARAMETERS > ## > > ############################################################# > > # Spherical boundary conditions > sphericalBC on > sphericalBCcenter 30.3081743413, 28.8049907121, > 15.353994423 > sphericalBCr1 26.0 > sphericalBCk1 10 > sphericalBCexp1 2 > > > > ############################################################# > ## EXECUTION SCRIPT > ## > > ############################################################# > > # Minimization > minimize 100 > reinitvels $temperature > > run 2500 ;# 5ps> > > > E-mail to subscribers: CHEMISTRY=-=ccl.net > =-=ccl.net > > or use:> > E-mail to administrators: CHEMISTRY-REQUEST=-=ccl.net > > =-=ccl.net > > or useConferences: > > http://server.ccl.net/chemistry/announcements/conferences/> > > > E-mail to subscribers: CHEMISTRY*_*ccl.net > or use:> > E-mail to administrators: CHEMISTRY-REQUEST*_*ccl.net > or useConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > From owner-chemistry@ccl.net Mon Feb 7 18:20:00 2011 From: "Theodore S. Dibble tsdibble ~ syr.edu" To: CCL Subject: CCL:G: IRC defective at low frequencies Message-Id: <-43899-110207171816-26339-wqbBvo1KvyyKDN6vxFYqyQ:server.ccl.net> X-Original-From: "Theodore S. Dibble" Date: Mon, 7 Feb 2011 17:18:06 -0500 Sent to CCL by: "Theodore S. Dibble" [tsdibble++syr.edu] Dario, Why do you need IRCs for these reactions; aren't the nature of the transition states obvious form animation of the imaginary frequencies? The small imaginary frequencies you have are tricky. Did you optimize the transition state with int=ultrafine? I would suggest keeping int=ultrafine in the irc calculation but dropping the vtight option from the irc command, as that will probably make it harder to optimize points on the irc. I presume that when you switched basis sets for the irc you used a transition state structure optimized with the larger basis set. Good Luck! Theodore S. Dibble Chemistry Department SUNY-Environmental Science and Forestry 1 Forestry Drive Syracuse, NY 13210 (315) 470-6596 (315) 470-6856 (fax) http://www.esf.edu/chemistry/faculty/dibble.htm > "Dario Fernando Coral Obando ferchocoralg16]-[gmail.com" wrote: > > Sent to CCL by: "Dario Fernando Coral Obando" [ferchocoralg16^_^gmail.com] > I work in the modeling of fragmentations of benzoazepines and, I found many conformational changes in the azepine ring. The transition states for these conformational changes usually have low frequencies (between 17 and 50) and for them, i could not get a quality IRC. They have no IRC maximum and only had 3 or at most 4 points, even though more points are specified in the input files. > > I used the Gaussian 09W package with the following route sections: > > # irc=(maxpoints=5,calcfc) ub3lyp/6-31g(d) > > # UB3LYP/6-31G(d) IRC=(CALCFC,MAXPOINTS=40,MAXCYCLE=20) SCF=DIRECT > > # irc=(maxpoints=10,calcfc,vtight,maxcycle=20,stepsize=1) ub3lyp/6-31+ g(d,p) int=ultrafine scf=direct > > It would be helpful if you guide me a little about how to calculate these IRC for conformational changes correctly. I'm starting on the topic of computer modeling of reactions and your contributions will be very valuables. > > Carefully > > Dario Fernando Coral Obando > Chemical student > Universidad de Nario, Pasto, Colombia > > From owner-chemistry@ccl.net Mon Feb 7 18:55:00 2011 From: "=?UTF-8?Q?Jaros=C5=82aw_Kalinowski?= kofeinu|a|gmail.com" To: CCL Subject: CCL:G: Optmization error Message-Id: <-43900-110207153817-11070-0V6HxAoqYkc5lVQ12Cluyw{}server.ccl.net> X-Original-From: =?UTF-8?Q?Jaros=C5=82aw_Kalinowski?= Content-Type: multipart/alternative; boundary=000e0cd152d4a70553049bb7350e Date: Mon, 7 Feb 2011 21:38:08 +0100 MIME-Version: 1.0 Sent to CCL by: =?UTF-8?Q?Jaros=C5=82aw_Kalinowski?= [kofeinu++gmail.com] --000e0cd152d4a70553049bb7350e Content-Type: text/plain; charset=UTF-8 Hi, I do not see the whole error but I think that simple setting to more cycles of optimization could help, i.e., try to change "OPT" to "OPT=(MaxCycles=200)". I am not an expert in the case of older gaussian but I suppose this particular keyword is the same as in the new one :-) 2011/2/7 Guilherme Luis Cordeiro guilhermecord|*|gmail.com < owner-chemistry:-:ccl.net> > > Sent to CCL by: "Guilherme Luis Cordeiro" [guilhermecord .. gmail.com] > Dear members, > > could anyone help me solve this optmization problem: > > Initial guess read from the read-write file: > Restarting incremental Fock formation. > Restarting incremental Fock formation. > Restarting incremental Fock formation. > >>>>>>>>>> Convergence criterion not met. > SCF Done: E(RHF) = -1097.91175446 A.U. after 65 cycles > Convg = 0.2394D-05 -V/T = 2.0014 > S**2 = 0.0000 > Convergence failure -- run terminated. > Error termination via Lnk1e in C:\G98W\l502.exe. > > My input was as follows: > > ********************************************* > Gaussian 98: x86-Win32-G98RevA.9 19-Apr-2000 > 06-Feb-2011 > ********************************************* > %mem=6MW > %nproc=1 > Will use up to 1 processors via shared memory. > %chk=Quercertina.chk > Default route: MaxDisk=2000MB > --------------------------- > #T RHF/6-31+G(d,p) Opt Test > --------------------------- > ---------------------- > Quercetin Optimization > ---------------------- > Symbolic Z-matrix: > Charge = 0 Multiplicity = 1 > C > C 1 B1 > C 2 B2 1 A1 > C 3 B3 2 A2 1 D1 0 > O 4 B4 3 A3 2 D2 0 > C 5 B5 4 A4 3 D3 0 > O 3 B6 2 A5 1 D4 0 > O 1 B7 2 A6 3 D5 0 > O 2 B8 1 A7 6 D6 0 > C 3 B9 2 A8 1 D7 0 > C 4 B10 3 A9 2 D8 0 > C 11 B11 4 A10 3 D9 0 > C 10 B12 3 A11 2 D10 0 > H 11 B13 4 A12 3 D11 0 > O 12 B14 11 A13 4 D12 0 > H 13 B15 10 A14 3 D13 0 > C 6 B16 5 A15 4 D14 0 > C 17 B17 6 A16 5 D15 0 > C 18 B18 17 A17 6 D16 0 > C 19 B19 18 A18 17 D17 0 > C 20 B20 19 A19 18 D18 0 > C 17 B21 6 A20 5 D19 0 > H 18 B22 17 A21 6 D20 0 > O 19 B23 18 A22 17 D21 0 > O 20 B24 19 A23 18 D22 0 > H 21 B25 20 A24 19 D23 0 > H 22 B26 17 A25 6 D24 0 > H 12 B27 11 A26 4 D25 0 > H 3 B28 2 A27 1 D26 0 > H 1 B29 2 A28 3 D27 0 > H 19 B30 18 A29 17 D28 0 > H 20 B31 19 A30 18 D29 0 > Variables: > B1 1.3728 > B2 1.42201 > B3 1.41887 > B4 1.42172 > B5 1.37334 > B6 2.45285 > B7 1.43 > B8 1.43 > B9 1.42203 > B10 1.42208 > B11 1.37286 > B12 1.37294 > B13 1.10035 > B14 1.43 > B15 1.09995 > B16 1.54 > B17 1.39516 > B18 1.39471 > B19 1.39543 > B20 1.39483 > B21 1.39483 > B22 1.09966 > B23 1.43 > B24 1.43 > B25 1.09976 > B26 1.0996 > B27 1.9702 > B28 3.24788 > B29 1.9702 > B30 1.9702 > B31 1.9702 > A1 120.50995 > A2 119.0959 > A3 119.21033 > A4 120.45591 > A5 90.92589 > A6 120.64768 > A7 120.8832 > A8 121.70036 > A9 119.05963 > A10 120.54905 > A11 120.49677 > A12 118.59132 > A13 120.64917 > A14 120.68504 > A15 120.64565 > A16 119.99722 > A17 120.00863 > A18 119.99417 > A19 119.99399 > A20 120.00432 > A21 119.98077 > A22 120.0128 > A23 119.98114 > A24 120.01134 > A25 120.008 > A26 147.99709 > A27 101.86544 > A28 93.29976 > A29 92.66488 > A30 92.63322 > D1 0.0171 > D2 -0.00956 > D3 -0.00404 > D4 -179.99446 > D5 179.99516 > D6 -179.99714 > D7 -179.98755 > D8 179.99469 > D9 0.00145 > D10 -179.99953 > D11 179.99838 > D12 179.98387 > D13 179.99873 > D14 -179.99903 > D15 0.03597 > D16 -179.97293 > D17 -0.05684 > D18 0.03411 > D19 -179.9693 > D20 -0.05203 > D21 179.96185 > D22 -179.99644 > D23 -179.99951 > D24 -0.00555 > D25 179.99535 > D26 -179.99566 > D27 179.99516 > D28 179.94629 > D29 -179.99835 > > Thanks.> > > -- Best Regards, J.Kalinowski. Theoretical Modeling of Chemical Processes Group Faculty of Chemistry, University of Wroclaw. 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quoted-printable Content-Type: text/plain; charset=us-ascii > Thanks. I do use Avogadro too. But when it comes to building = organometallic molecules like Ferrocene in which the connecting bonds = between the central atom and the ligands are to the aromatic pie = electrons and not really atoms, it becomes a problem using Avogadro. At the moment, Avogadro has a more "free-form" draw tool. It's a little = hard to make "free-form" intuitive for metallocenes. I've tried. I'm = currently working on a "click and insert" draw tool, which will be more = intuitive. In the meantime, I believe a few people have suggested ArgusLab to you = before. It's Windows-based, no cost, and can run some types of MOPAC = calculations. http://arguslab.com/ Best regards, -Geoff --- Prof. Geoffrey Hutchison Assistant Professor, Department of Chemistry University of Pittsburgh http://hutchison.chem.pitt.edu/ Office: (412) 648-0492 --Apple-Mail-1-1004298516 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii
Thanks. I do use Avogadro = too. But when it comes to building organometallic molecules like = Ferrocene in which the connecting bonds between the central atom and the = ligands are to the aromatic pie electrons and not really atoms, it = becomes a problem using = Avogadro.

At the moment, Avogadro = has a more "free-form" draw tool. It's a little hard to make "free-form" = intuitive for metallocenes. I've tried. I'm currently working on a = "click and insert" draw tool, which will be more = intuitive.

In the meantime, I believe a few = people have suggested ArgusLab to you before. It's Windows-based, no = cost, and can run some types of MOPAC = calculations.


Best regards,
-Geoff

---
Prof. Geoffrey = Hutchison
Assistant Professor, Department of = Chemistry
University of Pittsburgh

= --Apple-Mail-1-1004298516--