From owner-chemistry@ccl.net Mon Oct 22 09:26:01 2012 From: "Basma Ghazal basmaghazal|*|ymail.com" To: CCL Subject: CCL: problem in frequency calculation Message-Id: <-47783-121022091819-15743-0g5mx2hleO7IR4CVkNFxww!=!server.ccl.net> X-Original-From: Basma Ghazal Content-Type: multipart/alternative; boundary="-2079400718-600698486-1350911892=:88867" Date: Mon, 22 Oct 2012 06:18:12 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Basma Ghazal [basmaghazal ~ ymail.com] ---2079400718-600698486-1350911892=:88867 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hi: =0AFor calculation =E2=88=86Gsolvation of different dyes, I do optimiza= tion and frequency for a previously=0Acalculated dye (at the same level) co= ntains: 7 benzene rings, one positive Oxygen,=0Aand other negative Nitrogen= , calculated at #B3LYP/6-31+G(d,p) opt freq & Charge =3D0 =C2=A0Multiplicit= y =3D1, running on PC '' processor: corei7 &=0ARAM: 5 GB''. =0AThe optimiza= tion were done=0Aat =E2=80=99=E2=80=995=0Adays 16 hours 14 minutes 48.0 sec= onds=E2=80=9Dwhile, the frequency is stop without error at this step =0A=C2= =A0 =0A**** Warning!!: The=0Alargest alpha MO coefficient is 0.12905893D+03= =0A**** Warning!!: The=0Asmallest alpha delta epsilon is 0.58262457D-01 = =0ASymmetrizing basis deriv=0Acontribution to polar: =0AIMax=3D3 JMax=3D2 D= iffMx=3D=0A0.00D+00 =0AG2DrvN: will do 73=0Acenters at a time, making 1 pas= ses doing MaxLOS=3D2. =0ACalling FoFCou, ICntrl=3D=0A3107 FMM=3DT I1Cent=3D= 0. =0AFoFDir/FoFCou used for=0AL=3D0 through L=3D2. ''. =C2=A0 =0A=C2=A0 = =0AI add optcyc=3D400=0ASCF=3DXQC without=0Aany progress, So=C2=A0does anyo= ne have any Idea, how can i solve this problem to calculate frequency? =0A= =C2=A0 =0ARegards, =0A-----------------------------------=0ABasma S. Ghazal= =0AMSc. Organic Chemistry =0ATherapeutical Chemistry Department =0ANational= Research Center, Egypt. ---2079400718-600698486-1350911892=:88867 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
=0A= =0A=0A=0A
<= div style=3D"color: rgb(0, 0, 0); font-family: verdana, helvetica, sans-ser= if; font-size: 14pt; background-color: rgb(255, 255, 255);">
Hi:
=0A=0A
For calculati= on =E2=88=86Gsolvation=0Aof different dy= es, I do optimization and frequency for a previously=0Acalculated dye (at t= he same level) contains: 7 benzene rings, one positive Oxygen,=0Aand other = negative Nitrogen, calculated at #B3LYP/6-31+G(d,p) opt freq = & Charge =3D0  Multiplicity =3D1, running on PC '= ' processor: corei7 &=0ARAM: 5 GB''.
= =0A=0A
The optimization were done=0Aat =E2=80=99=E2=80=995=0Adays 16 hours 14 minutes 48.0 seconds=E2=80=9D  
=0A= =0A
**** Warning!!: The=0Alargest = alpha MO coefficient is 0.12905893D+03
=0A=0A
**** Warning!!: The=0Asmallest alpha delta eps= ilon is 0.58262457D-01
=0A=0A
Symmetrizing basis deriv=0Acontribution to polar: =0A=0A
IMax=3D3 JMax=3D2 Diff= Mx=3D=0A0.00D+00
=0A=0A
= G2DrvN: will do 73=0Acenters at a time, making 1 passes doing MaxLOS= =3D2.
=0A=0A
Call= ing FoFCou, ICntrl=3D=0A3107 FMM=3DT I1Cent=3D 0.
=0A=0AFoFDir/FoFCou used for=0AL=3D0 thro= ugh L=3D2. ''.  
=0A=0A
 
=0A=0A
<= span style=3D'color: black; font-family: "Verdana", "sans-serif";'>I add optcyc=3D400=0ASCF=3DXQC without=0Aany progress, So do= es anyone have any Idea, how can i solve this problem to calculate=0Afrequency?
=0A=0A
 
=0A=0A
Regards,
=0A=0A
=0A
----------------------= -------------
=0A
Basma S. Ghazal
MSc. Orga= nic Chemistry
=0A
Therapeutical Chemistry D= epartment
National Research Center, Egypt.


---2079400718-600698486-1350911892=:88867-- From owner-chemistry@ccl.net Mon Oct 22 11:47:01 2012 From: "Roger Robinson r.robinson*o*imperial.ac.uk" To: CCL Subject: CCL: Restart CCSD jobs Message-Id: <-47784-121022111052-17690-5c75bLucz3YvDPJO1fT9qA_+_server.ccl.net> X-Original-From: Roger Robinson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 22 Oct 2012 16:08:44 +0100 MIME-Version: 1.0 Sent to CCL by: Roger Robinson [r.robinson : imperial.ac.uk] Hi, I need to restart some CCSD jobs as the machine they are on are being decommissioned. The jobs have produced some very large rwf ie between 100GB and 270GB. I have copied the rwf files back from local sites to the network device. I notice the RWF havent been rewritten to for several days. They have all got to the part of the job after the convergence iterations ie all say something like this. Iteration Nr. 14 ********************** DD1Dir will call FoFDir 1 times, MxPair= 600 NAB= 300 NAA= 0 NBB= 0 NumPrc= 16. DE(Corr)= -1.5338361 E(CORR)= -349.45990574 Delta=-1.89D-08 NORM(A)= 0.12459143D+01 Largest amplitude= 3.48D-02 The scratch files have also stopped growing. Is there still alot of input and output to the scratch files anymore after this point ? Would it be possible to carry out the jobs with the scratch file on the network drive at this point ? I should I move then to new local file systems ? As a test I restarted one job with the restart file on the network file system. The job seems to be running ok and more importantly is using 100% of the CPU allocated which could suggest its not struggling for I/O throughtput ? Thanks Roger From owner-chemistry@ccl.net Mon Oct 22 12:22:00 2012 From: "Roger Robinson r.robinson-#-imperial.ac.uk" To: CCL Subject: CCL: Restart CCSD jobs Message-Id: <-47785-121022111243-17817-+0+zdxx0K8deVJ+wpDogQQ#server.ccl.net> X-Original-From: Roger Robinson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 22 Oct 2012 16:10:54 +0100 MIME-Version: 1.0 Sent to CCL by: Roger Robinson [r.robinson%x%imperial.ac.uk] Hi, I need to restart some CCSD jobs as the machine they are on are being decommissioned. The jobs have produced some very large rwf ie between 100GB and 270GB. I have copied the rwf files back from local sites to the network device. I notice the RWF havent been rewritten to for several days. They have all got to the part of the job after the convergence iterations ie all say something like this. Iteration Nr. 14 ********************** DD1Dir will call FoFDir 1 times, MxPair= 600 NAB= 300 NAA= 0 NBB= 0 NumPrc= 16. DE(Corr)= -1.5338361 E(CORR)= -349.45990574 Delta=-1.89D-08 NORM(A)= 0.12459143D+01 Largest amplitude= 3.48D-02 The scratch files have also stopped growing. Is there still alot of input and output to the scratch files anymore after this point ? Would it be possible to carry out the jobs with the scratch file on the network drive at this point ? I should I move then to new local file systems ? As a test I restarted one job with the restart file on the network file system. The job seems to be running ok and more importantly is using 100% of the CPU allocated which could suggest its not struggling for I/O throughtput ? Thanks Roger From owner-chemistry@ccl.net Mon Oct 22 12:57:00 2012 From: "Roger Robinson scu98rkr|*|gmail.com" To: CCL Subject: CCL: Restart CCSD jobs Message-Id: <-47786-121022112242-18421-j/0Ssb0yig7q0ppCQYmiaQ ~ server.ccl.net> X-Original-From: Roger Robinson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 22 Oct 2012 16:14:21 +0100 MIME-Version: 1.0 Sent to CCL by: Roger Robinson [scu98rkr^^gmail.com] Hi, I need to restart some CCSD jobs as the machine they are on are being decommissioned. The jobs have produced some very large rwf ie between 100GB and 270GB. I have copied the rwf files back from local sites to the network device. I notice the RWF havent been rewritten to for several days. They have all got to the part of the job after the convergence iterations ie all say something like this. Iteration Nr. 14 ********************** DD1Dir will call FoFDir 1 times, MxPair= 600 NAB= 300 NAA= 0 NBB= 0 NumPrc= 16. DE(Corr)= -1.5338361 E(CORR)= -349.45990574 Delta=-1.89D-08 NORM(A)= 0.12459143D+01 Largest amplitude= 3.48D-02 The scratch files have also stopped growing. Is there still alot of input and output to the scratch files anymore after this point ? Would it be possible to carry out the jobs with the scratch file on the network drive at this point ? I should I move then to new local file systems ? As a test I restarted one job with the restart file on the network file system. The job seems to be running ok and more importantly is using 100% of the CPU allocated which could suggest its not struggling for I/O throughtput ? Thanks Roger From owner-chemistry@ccl.net Mon Oct 22 13:32:00 2012 From: "Richard Harper drrwharper,+,gmail.com" To: CCL Subject: CCL: tinker - protein with ligands Message-Id: <-47787-121022112511-25945-D0CHp55iRhu+KC01Y8W4Kg^server.ccl.net> X-Original-From: Richard Harper Content-Type: multipart/alternative; boundary=e0cb4efe2aecf9144604cca774a8 Date: Mon, 22 Oct 2012 11:25:00 -0400 MIME-Version: 1.0 Sent to CCL by: Richard Harper [drrwharper++gmail.com] --e0cb4efe2aecf9144604cca774a8 Content-Type: text/plain; charset=ISO-8859-1 I want to model a protein with included ligands using TINKER. I presume that if I can get PDBXYZ to do the conversion to XYZ format, I can minimize, run dynamics, etc. PDBXYZ (using mm3pro.prm parameters) gave an XYZ file containing only the aminoacid residues. Is there a way to get it to include the ligands. The input is a homology of a protein with point mutations, based on a crystal structure with bound ligands (two of them). I want to get be sure I have a realistic structure for future work. Thanks for any help, Dick Harper Indiana University-Purdue University Indianapolis (IUPUI) --e0cb4efe2aecf9144604cca774a8 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable I want to model a protein with included ligands using TINKER.=A0 I presume = that if I can get PDBXYZ to do the conversion to XYZ format, I can minimize= , run dynamics, etc.
PDBXYZ (using mm3pro.prm parameters) gave an XYZ fi= le containing only the aminoacid residues.=A0 Is there a way to get it to i= nclude the ligands.=A0
The input is a homology of a protein with point mutations, based on a cryst= al structure with bound ligands (two of them).=A0 I want to get be sure I h= ave a realistic structure for future work.

Thanks for any help,
Dick Harper

Indiana University-Purdue University Indianapolis (IUPUI= )
--e0cb4efe2aecf9144604cca774a8-- From owner-chemistry@ccl.net Mon Oct 22 14:42:01 2012 From: "Van Dam, Hubertus J HubertusJJ.vanDam[A]pnnl.gov" To: CCL Subject: CCL: Restart CCSD jobs Message-Id: <-47788-121022130846-16345-+/EbPwLwHMxpl7ZvwtHawg- -server.ccl.net> X-Original-From: "Van Dam, Hubertus J" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 22 Oct 2012 10:08:35 -0700 MIME-Version: 1.0 Sent to CCL by: "Van Dam, Hubertus J" [HubertusJJ.vanDam|,|pnnl.gov] Hi Roger, I think what you are doing is probably alright. The main gotcha that you might run into is that the number representations might be different on different machines. However, as in recent years the number of different processor architectures in common use has decreased that is less of a problem today than it used to be. Having said that I have trouble pinpointing what bit of output you are looking at. If you want me to provide some more detailed comments could you send your input file, please? Best wishes, Huub van Dam Pacific Northwest National Laboratory Tel:  509-372-6441 -----Original Message----- > From: owner-chemistry+hubertus.vandam==pnnl.gov]*[ccl.net [mailto:owner-chemistry+hubertus.vandam==pnnl.gov]*[ccl.net] On Behalf Of Roger Robinson r.robinson*o*imperial.ac.uk Sent: Monday, October 22, 2012 8:09 AM To: Van Dam, Hubertus J Subject: CCL: Restart CCSD jobs Sent to CCL by: Roger Robinson [r.robinson : imperial.ac.uk] Hi, I need to restart some CCSD jobs as the machine they are on are being decommissioned. The jobs have produced some very large rwf ie between 100GB and 270GB. I have copied the rwf files back from local sites to the network device. I notice the RWF havent been rewritten to for several days. They have all got to the part of the job after the convergence iterations ie all say something like this. Iteration Nr. 14 ********************** DD1Dir will call FoFDir 1 times, MxPair= 600 NAB= 300 NAA= 0 NBB= 0 NumPrc= 16. DE(Corr)= -1.5338361 E(CORR)= -349.45990574 Delta=-1.89D-08 NORM(A)= 0.12459143D+01 Largest amplitude= 3.48D-02 The scratch files have also stopped growing. Is there still alot of input and output to the scratch files anymore after this point ? Would it be possible to carry out the jobs with the scratch file on the network drive at this point ? I should I move then to new local file systems ? As a test I restarted one job with the restart file on the network file system. The job seems to be running ok and more importantly is using 100% of the CPU allocated which could suggest its not struggling for I/O throughtput ? Thanks Rogerhttp://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 Oct 22 15:34:00 2012 From: "Paolo Tosco paolo.tosco-$-unito.it" To: CCL Subject: CCL: tinker - protein with ligands Message-Id: <-47789-121022145559-28057-ju4MYHdnXHJY6q6UkB2TYQ{:}server.ccl.net> X-Original-From: Paolo Tosco Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Mon, 22 Oct 2012 20:55:42 +0200 Mime-Version: 1.0 (1.0) Sent to CCL by: Paolo Tosco [paolo.tosco]=[unito.it] Dear Richard, SDF2XYZ2SDF (sdf2xyz2sdf.sourceforge.net) can do that using MMFF94 instead of MM3. HTH, Paolo -- ========================================================== Paolo Tosco, Ph.D. Department of Drug Science and Technology Via Pietro Giuria, 9 - 10125 Torino (Italy) Tel: +39 011 670 7680 | Mob: +39 348 5537206 Fax: +39 011 670 7687 | E-mail: paolo.tosco{=}unito.it http://open3dqsar.org | http://open3dalign.org ========================================================== On 22 Oct 2012, at 17:25, "Richard Harper drrwharper,+,gmail.com" wrote: > I want to model a protein with included ligands using TINKER. I presume that if I can get PDBXYZ to do the conversion to XYZ format, I can minimize, run dynamics, etc. > PDBXYZ (using mm3pro.prm parameters) gave an XYZ file containing only the aminoacid residues. Is there a way to get it to include the ligands. > The input is a homology of a protein with point mutations, based on a crystal structure with bound ligands (two of them). I want to get be sure I have a realistic structure for future work. > > Thanks for any help, > Dick Harper > > Indiana University-Purdue University Indianapolis (IUPUI) From owner-chemistry@ccl.net Mon Oct 22 19:43:00 2012 From: "Amy Austin amy_jean_austin---yahoo.com" To: CCL Subject: CCL:G: Restart CCSD jobs Message-Id: <-47790-121022175658-25198-brFwDM2sEJoBrV+3VzjTiA{:}server.ccl.net> X-Original-From: Amy Austin Content-Type: multipart/alternative; boundary="-244526598-895988976-1350943010=:67412" Date: Mon, 22 Oct 2012 14:56:50 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Amy Austin [amy_jean_austin . yahoo.com] ---244526598-895988976-1350943010=:67412 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi Roger,=0A=0AThe checkpoint files needed for reoptimization are hardware = specific. The best thing to do is to convert to .chk (which is a binary fil= e) to .fchk (asci file) using the formcheck utility.=0A=0Ae.g. =0A=0A$ form= chk example.chk example.fchk=0A=0Ahttp://www.gaussian.com/g_tech/g_ur/u_for= mchk.htm=0A=0AKind regards,=0A=0AAmy=0A=0A=0A=0A=0A=0A_____________________= ___________=0A From: Roger Robinson r.robinson*o*imperial.ac.uk =0ATo: "Austin, Amy J " = =0ASent: Monday, October 22, 2012 11:08 AM=0ASubject: CCL: Restart CCSD job= s=0A =0A=0ASent to CCL by: Roger Robinson [r.robinson : imperial.ac.uk]=0AH= i,=0A=0AI need to restart some CCSD jobs as the machine they are on are bei= ng decommissioned.=0A=0AThe jobs have produced some very large rwf ie betwe= en 100GB and 270GB.=0A=0AI have copied the rwf files back from local sites = to the network device.=0A=0AI notice the RWF havent been rewritten to for s= everal days.=0A=0AThey have all got to the part of the job after the conver= gence iterations ie all say something like this.=0A=0AIteration Nr.=A0 14= =0A**********************=0ADD1Dir will call FoFDir=A0 1 times, MxPair=3D= =A0 =A0 =A0 600=0ANAB=3D=A0 300 NAA=3D=A0 =A0 0 NBB=3D=A0 =A0 0 NumPrc= =3D 16.=0ADE(Corr)=3D=A0 -1.5338361=A0 =A0 E(CORR)=3D=A0 =A0 -349.4599057= 4 Delta=3D-1.89D-08=0ANORM(A)=3D=A0 0.12459143D+01=0ALargest amplitude=3D = 3.48D-02=0A=0AThe scratch files have also stopped growing.=0A=0AIs there st= ill alot of input and output to the scratch files anymore after this point = ?=0A=0AWould it be possible to carry out the jobs with the scratch file on = the network drive at this point ?=A0 I should I move then to new local file= systems ?=0A=0AAs a test I restarted one job with the restart file on the = network file system. The job seems to be running ok and more importantly is= using 100% of the CPU allocated which could suggest its not struggling for= I/O throughtput ?=0A=0AThanks Roger=0A=0A=0A=0A-=3D This is automatically = added to each message by the mailing script =3D-=0ATo recover the email add= ress of the author of the message, please change=0Athe strange characters o= n the top line to the ^_^ sign. You can also=0Alook up the X-Original-From: l= ine in the mail header.=0A=0AE-mail to subscribers: CHEMISTRY^_^ccl.net or us= e:=0A=A0 =A0=0A=0AE-mail t= o administrators: CHEMISTRY-REQUEST^_^ccl.net or use=0A=A0 =A0 http://www.ccl= .net/cgi-bin/ccl/send_ccl_message=0A=0ASubscribe/Unsubscribe:=A0 =A0 =A0 ht= tp://www.ccl.net/chemistry/sub_unsub.shtml=0A=0ABefore posting, check wait = time at: http://www.ccl.net=0A=0AConferences: = http://server.ccl.net/chemistry/announcements/conferences/=0A=0ASearch Mess= ages: http://www.ccl.net/chemistry/searchccl/index.shtml=0A=0AIf your mail = bounces from CCL with 5.7.1 error, check:=0A=A0 =A0 http://www.ccl.net/spa= mmers.txt=0A=0A---244526598-895988976-1350943010=:67412 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hi Roger,

The = checkpoint files needed for reoptimization are hardware specific. The best = thing to do is to convert to .chk (which is a binary file) to .fchk (asci f= ile) using the formcheck utility.

e.g. 
$ formchk exa=
mple.chk example.fchk

http://www.gaussian.com/g_tech/g_ur/u_f=
ormchk.htm

Kind regards,

Amy

<= /span>

From: Roger Robinson r.robinson*= o*imperial.ac.uk <owner-chemistry^_^ccl.net>
To: "Austin, Amy J " <amy_jean_austin^_^yahoo.c= om>
Sent: Monday, = October 22, 2012 11:08 AM
Subject= : CCL: Restart CCSD jobs

=0A
Sent to C= CL by: Roger Robinson [r.robinson : imperial.ac.uk]
Hi,

I need to restart some CCSD= jobs as the machine they are on are being decommissioned.

The jobs = have produced some very large rwf ie between 100GB and 270GB.

I have= copied the rwf files back from local sites to the network device.

I= notice the RWF havent been rewritten to for several days.

They have= all got to the part of the job after the convergence iterations ie all say= something like this.

Iteration Nr.  14
******************= ****
DD1Dir will call FoFDir  1 times, MxPair=3D    &nb= sp; 600
NAB=3D  300 NAA=3D    0 NBB=3D    = 0 NumPrc=3D 16.
DE(Corr)=3D  -1.5338361    E(CORR)=3D&n= bsp;   -349.45990574 Delta=3D-1.89D-08
NORM(A)=3D  0.124591= 43D+01
Largest amplitude=3D 3.48D-02

The scratch files have also stopped growing.

Is there still alot of input and output to the scr= atch files anymore after this point ?

Would it be possible to carry = out the jobs with the scratch file on the network drive at this point ?&nbs= p; I should I move then to new local file systems ?

As a test I rest= arted one job with the restart file on the network file system. The job see= ms to be running ok and more importantly is using 100% of the CPU allocated= which could suggest its not struggling for I/O throughtput ?

Thanks= Roger



-=3D This is automatically added to each message by t= he 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:
   = ;

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---244526598-895988976-1350943010=:67412-- From owner-chemistry@ccl.net Mon Oct 22 20:17:01 2012 From: "Walter Ca on wcanon*_*ciq.uchile.cl" To: CCL Subject: CCL: S^2 for a antiferromagnetic system of 6 Fe(III) Message-Id: <-47791-121022160736-4141-x/f/xG06zsHhhINLG9EALg_-_server.ccl.net> X-Original-From: "Walter Ca on" Date: Mon, 22 Oct 2012 16:07:34 -0400 Sent to CCL by: "Walter Ca on" [wcanon#ciq.uchile.cl] Dear CCl users, can anyone tell me, what is the S^2 value for a antiferromagnetic system of 6 Fe(III) system? thanks in advance Walter