From owner-chemistry@ccl.net Tue Jun 5 02:54:00 2012 From: "emmie aulakh emmie.aulakh[A]gmail.com" To: CCL Subject: CCL: How to calculate the EDA Message-Id: <-47029-120605025242-18018-vFtqyEp/HkEUv2UrTnsh4Q^^^server.ccl.net> X-Original-From: emmie aulakh Content-Type: multipart/alternative; boundary=20cf307f3af04f25bb04c1b418c8 Date: Tue, 5 Jun 2012 12:22:32 +0530 MIME-Version: 1.0 Sent to CCL by: emmie aulakh [emmie.aulakh ~ gmail.com] --20cf307f3af04f25bb04c1b418c8 Content-Type: text/plain; charset=ISO-8859-1 Respected Sir Thanks for the reply. Bt as far as I know Morokuma EDA does not calculate dispersion component. Am I wrong? On Mon, Jun 4, 2012 at 10:39 PM, Mehdi Esrafili m_esrafili.(!).yahoo.com < owner-chemistry(!)ccl.net> wrote: > You may use GAMESS program for energy decomposition analysis (EDA) based > on Morokuma method. This program is free of charge and also has > windows/linux version. > Sincerely > Mehdi > > > > ------------------------------------------------------------------------------------------------------------------------------ > `The man who makes no mistakes does not usually make anything.' > Edward John Phelps (1822-1900) > ------------------------------------------------------------------------------------------------------------------------------ > > Mehdi D. Esrafili, Ph.D. > Assistant Professor of Physical Chemistry > *Current address*: Department of Chemistry, > Faculty of Basic Sciences,University of > Maragheh, Iran. > E-mail 1: m_esrafili*yahoo.com > E-mail 2: esrafili*maragheh.ac.ir > > ------------------------------------------------------------------------------------------------------------------------------ > > ------------------------------ > *From:* "Darpan Aulakh darpan.aulakh2011-,-gmail.com" ccl.net> > *To:* "Esrafili, Mehdi D " > *Sent:* Saturday, June 2, 2012 3:27 PM > *Subject:* CCL: How to calculate the EDA > > Dear All > I want to carry out the energy decomposition analysis (especially to > calculate the dispersion component). Is SAPT the only way?? Can anyone > suggest any other windows based software to complete the purpose? > Thanks in advance. > > > > --20cf307f3af04f25bb04c1b418c8 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Respected Sir
Thanks for the reply. Bt as far as I know Morokuma EDA doe= s not calculate dispersion component. Am I wrong?

On Mon, Jun 4, 2012 at 10:39 PM, Mehdi Esrafili m_esrafili.(!).yahoo.com <owner-chemistry(!)ccl.net&g= t; wrote:
You may use GAMESS progr= am for energy decomposition analysis (EDA) based on Morokuma method. This p= rogram is free of charge and also has windows/linux version.
Sincerely
Mehdi
=
=A0
=A0
---------------------------------------------------= ---------------------------------------------------------------------------= =A0=A0
`The= man who makes no mistakes does not usually make anything.'
=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=A0=A0=A0=A0=A0 Edward John Phelps (1822-1900)
----= ---------------------------------------------------------------------------= -----------------------------------------------
Mehdi D. Esrafili, Ph.D= .
Assi= stant Professor of Physical Chemistry=A0
Current address:=A0Depar= tment of Chemistry,
Faculty of Basic Sciences,University of=
Mara= gheh, Iran.
E-mail 1: m_esrafili*yaho= o.com
E-mail 2: esrafili*maragheh.ac.ir
= ----------------------------------= ---------------------------------------------------------------------------= -----------------

From: "Darpan Aulakh = darpan.aulakh2011-,-gmail.co= m" <owner-chemistry*ccl.net>
To: "Esrafili, Mehdi D= " <m_esrafili*yahoo.com>
Sent:<= /b> Saturday, June 2, 2012 3:27 PM
Subject: CCL: How to calcul= ate the EDA

Dear All
I want to carry out the energy decomposition analysis (esp= ecially to calculate the dispersion component). Is SAPT the only way?? Can = anyone suggest any other windows based software to complete the purpose? =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=A0 Thanks in advance.




--20cf307f3af04f25bb04c1b418c8-- From owner-chemistry@ccl.net Tue Jun 5 05:42:00 2012 From: "Robert Perkins cclnanolab%a%gmail.com" To: CCL Subject: CCL: G09 Partial Optimization Message-Id: <-47030-120605054048-28513-D5Xbr2dKxWzVT9JZE8IaRg|a|server.ccl.net> X-Original-From: Robert Perkins Content-Type: multipart/alternative; boundary=f46d04088c758d086204c1b671c5 Date: Tue, 5 Jun 2012 14:10:40 +0430 MIME-Version: 1.0 Sent to CCL by: Robert Perkins [cclnanolab!^!gmail.com] --f46d04088c758d086204c1b671c5 Content-Type: text/plain; charset=ISO-8859-1 Hello I have tried partial optimization of a large molecule using several methods. *********** 1) Opt=ReedFreeze as follows (coordinates of the atoms 14,28,29 should be fixed during optimization) # ub3lyp/6-31G(d) opt=readfreeze scf(maxcycle=2048) nosymm Geometry Optimization using Opt= ReadFreeze 1 2 C -1.33169400 -7.86662672 -0.25217479 C 1.02891050 -8.07797168 -0.05038138 C 0.68951297 -6.66718478 -0.02839284 [...] H -0.92921784 -2.15470280 -0.78759023 noatoms atoms=1-63 notatoms=14,28,29 However, I get the following error in the output file GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization. NTrRot= 270 NTRed= 459 NAtoms= 63 NSkip= 270 IsLin=F Error in internal coordinate system. Error termination via Lnk1e in /home/nanolab//g09/l103.exe at Mon Jun 4 09:05:53 2012. Job cpu time: 0 days 1 hours 48 minutes 54.0 seconds. File lengths (MBytes): RWF= 245 Int= 0 D2E= 0 Chk= 7 Scr= 1 On the other hand, the full optimization of the same coordinates is done successfully, without any error in the internal coordinate system. *********** 2) Alternatively the POPT keyword does not work as follows # ub3lyp/6-31G(d) Popt scf(maxcycle=2048) nosymm Partial Optimization of cation 1 2 C 0 -1.33169400 -7.86662672 -0.25217479 C 0 1.02891050 -8.07797168 -0.05038138 C 0 0.68951297 -6.66718478 -0.02839284 [...] [-1 for fixed coordinates] H 0 -0.92921784 -2.15470280 -0.78759023 *********** 3) But the Opt=Z-matrix works, however, it takes a long time to arrange the coordinates and variables as C 0 x1 y1 z1 C 0 x2 y2 z2 C 0 x3 y3 z3 [...] Variables: x1 = -1.33169400 y1= -7.86662672 [..] Constants: ... Do you have any suggestion? Are the above codes correct in G09? Thanks RP --f46d04088c758d086204c1b671c5 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hello
I have tried partial optimization of a large molecule using severa= l methods.

***********
1) Opt=3DReedFreeze as follows (coordinate= s of the atoms 14,28,29 should be fixed during optimization)


# u= b3lyp/6-31G(d) opt=3Dreadfreeze scf(maxcycle=3D2048) nosymm

Geometry Optimization using Opt=3D ReadFreeze

1 2
=A0C=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 -1.33169400=A0=A0 -7.86662672=A0= =A0 -0.25217479
=A0C=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 = 1.02891050=A0=A0 -8.07797168=A0=A0 -0.05038138
=A0C=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.68951297=A0=A0 -6.66718478=A0=A0 -0.028392= 84
=A0[...]
=A0H=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 -0.9292178= 4=A0=A0 -2.15470280=A0=A0 -0.78759023
=A0
=A0noatoms atoms=3D1-63 not= atoms=3D14,28,29

However, I get the following error in the output fi= le

GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad= GradGrad
=A0Berny optimization.
=A0NTrRot=3D=A0=A0 270 NTRed=3D=A0=A0 459 NAtoms= =3D=A0=A0=A0 63 NSkip=3D=A0=A0 270 IsLin=3DF
=A0Error in internal coordi= nate system.
=A0Error termination via Lnk1e in /home/nanolab//g09/l103.e= xe at Mon Jun=A0 4 09:05:53 2012.
=A0Job cpu time:=A0 0 days=A0 1 hours 48 minutes 54.0 seconds.
=A0File l= engths (MBytes):=A0 RWF=3D=A0=A0=A0 245 Int=3D=A0=A0=A0=A0=A0 0 D2E=3D=A0= =A0=A0=A0=A0 0 Chk=3D=A0=A0=A0=A0=A0 7 Scr=3D=A0=A0=A0=A0=A0 1

On th= e other hand, the full optimization of the same coordinates is done success= fully, without any error in the internal coordinate system.

***********
2) Alternatively the POPT keyword does not work as follo= ws

# ub3lyp/6-31G(d) Popt scf(maxcycle=3D2048) nosymm

Partial Optimization of cation

1 2
=A0C=A0=A0 0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 -1.33169400=A0=A0 -7.8666= 2672=A0=A0 -0.25217479
=A0C=A0=A0 0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 1.02891050=A0=A0 -8.07797= 168=A0=A0 -0.05038138
=A0C=A0=A0 0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.68951297=A0=A0 -6.66718= 478=A0=A0 -0.02839284
=A0[...] [-1 for fixed coordinates]
=A0H=A0=A0 0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 -0.92921784=A0=A0 -2.1547= 0280=A0=A0 -0.78759023

***********
3) But the Opt=3DZ-matrix work= s, however, it takes a long time to arrange the coordinates and variables a= s

C 0 x1 y1 z1
C 0 x2 y2 z2
C 0 x3 y3 z3
[...]
Variables:
x1 =3D -1.33169400
y1=3D -7.86662= 672
[..]
Constants:
...

Do you have any suggestion? Are the= above codes correct in G09?
Thanks
RP


--f46d04088c758d086204c1b671c5-- From owner-chemistry@ccl.net Tue Jun 5 06:16:01 2012 From: "Ernst Horkel ehorkel(!)ioc.tuwien.ac.at" To: CCL Subject: CCL:G: keto-enol-problems Message-Id: <-47031-120605061148-628-DKwUDmLUpsr5uDvFVFM7BQ . server.ccl.net> X-Original-From: "Ernst Horkel" Date: Tue, 5 Jun 2012 06:11:46 -0400 Sent to CCL by: "Ernst Horkel" [ehorkel : ioc.tuwien.ac.at] Dear all, I have a (at least to me) strange problem when I try to describe a keto-enol tautomerism. The substance under inverstigation is a beta-keto carboxylic acid amide derivative; there is one possible keto-tautomer (having the ketone and the amide a C=O bond). Between the two possible enol-tautomers (one having the O-H on carbon C3 and the other having the O-H on the amide C1), there should be a transition state; I thik I found it, being planar in geometry with the hydrogen oszillating between the two oxygen atoms. A frequency run returned one single imaginary frequency with v=-1086cm-1. So this seems to make sence to me, right? But now the problem: in order to get the both tautomers connected via this TS, I followed the imag.freq. in both directions (manual displacement in gauss view, both in positive and negative direction) and optimized those structures. Results are chemically correct tautomers, frequency runs showed no imaginary frequency. BUT: in one of the tautomers, the gibbs free energy is HIGHER than in the TS! How is this possible? Does that make sence (I don't think so). Please help me and leave comments on this, as I'm really stucking at this point for a while. some background: *planned investigation: realative stability of two tautomers; calculation of the activation energy of the tautomerization. *used software: Gaussian 09, GaussView 5.0 on a Linux system *level of theory: DFT, M06-2X, 6-311G(d,p)++, solvent H2O, PCM theory *input (representative): "opt=tight freq 6-311++g(d,p) scrf=(solvent=water) geom=connectivity int=ultrafine m062x" *for calculation of "delta G" I used the calculated values in the ".log" file printed in the line (e.g.): "Sum of electronic and thermal Free Energies= -670.274904" So please can anyone help (guide) me out of this. Any helpful ideas or comments are really welcome. Thank You all in advance, best reagrds Ernst From owner-chemistry@ccl.net Tue Jun 5 07:33:01 2012 From: "Christina Jenifer msc christinamsc]^[gmail.com" To: CCL Subject: CCL: Software to superimpose XRD and optimized structures Message-Id: <-47032-120605011224-12915-fP2ARbDalyuVwuscDc1M5Q,+,server.ccl.net> X-Original-From: "Christina Jenifer msc" Date: Tue, 5 Jun 2012 01:12:21 -0400 Sent to CCL by: "Christina Jenifer msc" [christinamsc|a|gmail.com] Dear CClers I'm currently exploring computational softwares for Atom-by-atom superimposition of the optimized structures over the X-ray structure. So that I would like to ask for advice if there's any suitable software to superimpose this two structures? Kindly help me in this regard. Thanks in advance With Regards Christina From owner-chemistry@ccl.net Tue Jun 5 08:08:00 2012 From: "Max j J Prendergast eneas{}usal.es" To: CCL Subject: CCL: Initrot Problem in Tinker Message-Id: <-47033-120605074137-4643-Z+govhv+cFrGMa6Et5GKfg^server.ccl.net> X-Original-From: "Max j J Prendergast" Date: Tue, 5 Jun 2012 07:41:35 -0400 Sent to CCL by: "Max j J Prendergast" [eneas++usal.es] Hi everyone, im trying to perform a conformational search of indomethacin using the SCAN application of Tinker. Ive draw it with Chem3D and later transform the sdf file to xyz with MMFF atom types using sdf2tinkerxyz. The ANALYZE program runs without problems, but when ive started the SCAN routine, a message appeared: INITROT: rotation in atoms 10 and 11 occurs more than once in Z-matrix Tinker is unable to continue. Ive checked the atom types again and again, but its ok. Any idea of how to fix it? Thanks a lot. From owner-chemistry@ccl.net Tue Jun 5 09:30:00 2012 From: "Michel Petitjean petitjean.chiral||gmail.com" To: CCL Subject: CCL: Software to superimpose XRD and optimized structures Message-Id: <-47034-120605083249-16981-aNtca1aanmyfriURJUlwgA]-[server.ccl.net> X-Original-From: Michel Petitjean Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 5 Jun 2012 14:32:41 +0200 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral _ gmail.com] Dear Christina, If you know the pairwise correspondence, try ARMS (or POSE if the 3D alignment is already done). If you don't, try CSR (works with different molecules). All these freewares are available from: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html Best regards, Michel. MTi, INSERM UMR-S 973, University Paris 7, 35 rue Helene Brion, 75205 Paris Cedex 13, France. Phone: +331 5727 8434; Fax: +331 5727 8372 E-mail: petitjean.chiral**gmail.com (preferred), michel.petitjean**univ-paris-diderot.fr http://petitjeanmichel.free.fr/itoweb.petitjean.html 2012/6/5 Christina Jenifer msc christinamsc]^[gmail.com : > > Sent to CCL by: "Christina Jenifer msc" [christinamsc|a|gmail.com] > Dear CClers > >           I'm currently exploring computational softwares for Atom-by-atom superimposition of the optimized structures over the X-ray structure. So that I would like to ask for advice if there's any suitable software to superimpose this two structures? Kindly help me in this regard. > > Thanks in advance > > With Regards > Christina From owner-chemistry@ccl.net Tue Jun 5 10:05:00 2012 From: "Paolo Tosco paolo.tosco-*-unito.it" To: CCL Subject: CCL: Software to superimpose XRD and optimized structures Message-Id: <-47035-120605083554-19879-PQGpG1Rv7ihgw84RWXtJxA]^[server.ccl.net> X-Original-From: Paolo Tosco Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 05 Jun 2012 14:35:07 +0200 MIME-Version: 1.0 Sent to CCL by: Paolo Tosco [paolo.tosco*_*unito.it] Dear Christina, you may use Open3DALIGN for this purpose, which carries out atom-based superimpositions of 3D structures: http://open3dalign.org OpenBabel (included in the Open3DALIGN distribution) will convert your input files to SDF format, if needed. Cheers, Paolo On 06/05/2012 07:12 AM, Christina Jenifer msc christinamsc]^[gmail.com wrote: > Sent to CCL by: "Christina Jenifer msc" [christinamsc|a|gmail.com] > Dear CClers > > I'm currently exploring computational softwares for Atom-by-atom superimposition of the optimized structures over the X-ray structure. So that I would like to ask for advice if there's any suitable software to superimpose this two structures? Kindly help me in this regard. > > Thanks in advance > > With Regards > Christina> > -- ========================================================== Paolo Tosco, Ph.D. Phone: +39 011 6707680 Department of Drug Science Fax: +39 011 6707687 and Technology Mob: +39 348 5537206 Via Pietro Giuria, 9 10125 Torino, Italy http://open3dalign.org E-mail: paolo.tosco_-_unito.it http://open3dqsar.org ========================================================== From owner-chemistry@ccl.net Tue Jun 5 10:40:00 2012 From: "berger..chem.helsinki.fi" To: CCL Subject: CCL: Software to superimpose XRD and optimized structures Message-Id: <-47036-120605090238-13396-Lde0Ek0IJ9YKJN6fhRcipw-$-server.ccl.net> X-Original-From: berger**chem.helsinki.fi Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Tue, 5 Jun 2012 16:02:23 +0300 MIME-Version: 1.0 Sent to CCL by: berger:+:chem.helsinki.fi hi gOpenmol is able to that. id you choose proper settings, the coordianates afetr superimposing can be exported as well. cheers > > Sent to CCL by: "Christina Jenifer msc" [christinamsc|a|gmail.com] > Dear CClers > > I'm currently exploring computational softwares for > Atom-by-atom superimposition of the optimized structures over > the X-ray structure. So that I would like to ask for advice if > there's any suitable software to superimpose this two > structures? Kindly help me in this regard. > > Thanks in advance > > With Regards > Christina> > > From owner-chemistry@ccl.net Tue Jun 5 11:14:00 2012 From: "Andrew Yeung andrew.yeung]^[chem.tamu.edu" To: CCL Subject: CCL:G: keto-enol-problems Message-Id: <-47037-120605101551-17850-0QggVih4A0A3ONbozeSTCg(a)server.ccl.net> X-Original-From: Andrew Yeung Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 05 Jun 2012 09:15:43 -0500 MIME-Version: 1.0 Sent to CCL by: Andrew Yeung [andrew.yeung,,chem.tamu.edu] Just a thought. In the gas phase, the oscillating hydrogen species is probably the TS of the isomerization. In solution state, trace acid or base should catalyze the tautomerization? Andrew Yeung Donald J. Darensbourg Research Group Department of Chemistry, Texas A&M University 3255 TAMU College Station, TX 77843-3255 Tel: 979 845 4837 On 2012-06-05 5:11 AM, Ernst Horkel ehorkel(!)ioc.tuwien.ac.at wrote: > Sent to CCL by: "Ernst Horkel" [ehorkel : ioc.tuwien.ac.at] > Dear all, > > I have a (at least to me) strange problem when I try to describe a keto-enol tautomerism. The substance under inverstigation is a beta-keto carboxylic acid amide derivative; there is one possible keto-tautomer (having the ketone and the amide a C=O bond). Between the two possible enol-tautomers (one having the O-H on carbon C3 and the other having the O-H on the amide C1), there should be a transition state; I thik I found it, being planar in geometry with the hydrogen oszillating between the two oxygen atoms. A frequency run returned one single imaginary frequency with v=-1086cm-1. So this seems to make sence to me, right? But now the problem: in order to get the both tautomers connected via this TS, I followed the imag.freq. in both directions (manual displacement in gauss view, both in positive and negative direction) and optimized those structures. Results are chemically correct tautomers, frequency runs showed no imaginary frequency. BUT: in one of the tautomers, the gi! > bbs free energy is HIGHER than in the TS! How is this possible? Does that make sence (I don't think so). Please help me and leave comments on this, as I'm really stucking at this point for a while. > > some background: > > *planned investigation: realative stability of two tautomers; calculation of the activation energy of the tautomerization. > *used software: Gaussian 09, GaussView 5.0 on a Linux system > *level of theory: DFT, M06-2X, 6-311G(d,p)++, solvent H2O, PCM theory > *input (representative): "opt=tight freq 6-311++g(d,p) scrf=(solvent=water) geom=connectivity int=ultrafine m062x" > *for calculation of "delta G" I used the calculated values in the ".log" file printed in the line (e.g.): "Sum of electronic and thermal Free Energies= -670.274904" > > So please can anyone help (guide) me out of this. Any helpful ideas or comments are really welcome. > > Thank You all in advance, > > best reagrds > > Ernst> > From owner-chemistry@ccl.net Tue Jun 5 11:49:00 2012 From: "Mehdi Esrafili m_esrafili _ yahoo.com" To: CCL Subject: CCL: How to calculate the EDA Message-Id: <-47038-120605102232-748-FTXi51Bp2IOE0vnDhT/gXA~!~server.ccl.net> X-Original-From: Mehdi Esrafili Content-Type: multipart/alternative; boundary="1018391901-781171275-1338906141=:35106" Date: Tue, 5 Jun 2012 07:22:21 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Mehdi Esrafili [m_esrafili++yahoo.com] --1018391901-781171275-1338906141=:35106 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Emmie:=0AYou are right. Morokuma method is based on HF, so it does not= calculate dispersion energy. But, if you use Moller-Plesset (MPn) or Coupl= ed-Cluster (CC) correlated methods, dispersion energy may be evaluated by E= disp=3DEint(MPn or CC)-Eint(HF). But if you use DFT methods, you can not us= e this strategy. So, you may use=A0 RUNTYP=3DEDA route and "$LMOEDA" group = in GAMESS. See P. Su, and H. Li "Energy decomposition analysis of covalent = bonds and intermolecular=0Ainteractions" J. Chem. Phys. 131, 014102 2009. = =0ASincerely=0AMehdi=0A=0A=A0=0A-------------------------------------------= ---------------------------------------------------------------------------= --------=A0=A0=0A`The man who makes no mistakes does not usually make anyth= ing.'=0A=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=A0=A0=A0=A0=A0 Edward John Phelps (1822-1900)=0A--------= ---------------------------------------------------------------------------= ------------------------------------------- =0AMehdi D. Esrafili, Ph.D.=0AA= ssistant Professor of Physical Chemistry=A0=0ACurrent address:=A0Department= of Chemistry, =0AFaculty of Basic Sciences,University of=0AMaragheh, Iran.= =0AE-mail 1:m_esrafili~~yahoo.com=0AE-mail 2: esrafili~~maragheh.ac.ir=0A---= ---------------------------------------------------------------------------= ------------------------------------------------ =0A=0A=0A_________________= _______________=0A From: emmie aulakh emmie.aulakh[A]gmail.com =0ATo: "Esrafili, Mehdi D " =0A= Sent: Tuesday, June 5, 2012 11:22 AM=0ASubject: CCL: How to calculate the E= DA=0A =0A=0ARespected Sir=0AThanks for the reply. Bt as far as I know Morok= uma EDA does not calculate dispersion component. Am I wrong?=0A=0A=0AOn Mon= , Jun 4, 2012 at 10:39 PM, Mehdi Esrafili m_esrafili.^-^.yahoo.com wrote:=0A=0AYou may use GAMESS program for energy decom= position analysis (EDA) based on Morokuma method. This program is free of c= harge and also has windows/linux version.=0A>=0A>Sincerely=0A>Mehdi=0A>=A0= =0A>=A0=0A>----------------------------------------------------------------= --------------------------------------------------------------=A0=A0=0A>`Th= e man who makes no mistakes does not usually make anything.'=0A>=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= =A0=A0=A0=A0=A0 Edward John Phelps (1822-1900)=0A>-------------------------= ---------------------------------------------------------------------------= -------------------------- =0A>Mehdi D. Esrafili, Ph.D.=0A>Assistant Profes= sor of Physical Chemistry=A0=0A>Current address:=A0Department of Chemistry,= =0A>Faculty of Basic Sciences,University of=0A>Maragheh, Iran. =0A>E-mail = 1:m_esrafili*yahoo.com=0A>E-mail 2: esrafili*maragheh.ac.ir=0A>------------= ---------------------------------------------------------------------------= --------------------------------------- =0A>=0A>=0A>=0A>___________________= _____________=0A> From: "Darpan Aulakh darpan.aulakh2011-,-gmail.com" =0A>To: "Esrafili, Mehdi D " =0A= >Sent: Saturday, June 2, 2012 3:27 PM=0A>Subject: CCL: How to calculate the= EDA=0A> =0A>=0A>Dear All=0A>I want to carry out the energy decomposition a= nalysis (especially to calculate the dispersion component). Is SAPT the onl= y way?? Can anyone suggest any other windows based software to complete the= purpose?=0A>=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=A0 Thanks in advance.=0A>=0A>=0A>=0A> --1018391901-781171275-1338906141=:35106 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Emmie= :
You are right. Morokuma method is based on HF, so = it does not calculate dispersion energy. But, if you use Moller-Plesset (MP= n) or Coupled-Cluster (CC) correlated methods, dispersion energy may be eva= luated by Edisp=3DEint(MPn or CC)-Eint(HF). But if you use DFT methods, you= can not use this strategy. So, you may use  RUNTYP=3DEDA route and "$= LMOEDA" group in GAMESS. See P. Su, and H. Li "E= nergy decomposition analysis of covalent bonds and intermolecular
intera= ctions" J. Chem. Phys. 131, 014102 2009.
Sincerely=
Mehdi
 
---------------------------------------------------------------= ---------------------------------------------------------------  =
`The man who makes no mistakes does not usually make anything.'
           &n= bsp;            = ;          Edward John Phelps = (1822-1900)
-------------------------------------------------------= ----------------------------------------------------------------------- Mehdi D. Esrafili, Ph.D.
Assistant Professor of Physical Chemistry 
Current address: Department of Chemistry, <= /font>
Faculty of Basic Sciences,University of
Maragheh, Iran.
E-mail 1: m_e= srafili~~yahoo.com
E-mail 2: esrafili~~maragheh.ac.ir
-------------------------------------------------= ---------------------------------------------------------------------------= --

From: emmie aulakh emmie.aulakh[A]gmail.com <= ;owner-chemistry~~ccl.net>
To:<= /span> "Esrafili, Mehdi D " <m_esrafili~~yahoo.com>
<= b>Sent: Tuesday, June 5, 2012= 11:22 AM
Subject: CCL= : How to calculate the EDA

=0A
Respected Sir
Thanks for the reply. Bt as far as I know Morokuma EDA= does not calculate dispersion component. Am I wrong?

On Mon, Jun 4, 2012 at 10:39 PM, Mehdi Esrafili m= _esrafili.^-^.yahoo.com <owner-chemistry^-^ccl.net> wrote:
=0A
You may u= se GAMESS program for energy decomposition analysis (EDA) based on Morokuma= method. This program is free of charge and also has windows/linux version.=
=0A
Sincerely
Mehdi
 
 
--------------------------------------= ---------------------------------------------------------------------------= -------------  
=0A
`The man who makes no mistakes does no= t usually make anything.'
       = ;            &n= bsp;            = ;  Edward John Phelps (1822-1900)
=0A
-------------------------= ---------------------------------------------------------------------------= --------------------------
Mehdi D. Esrafili, Ph.D.
=0AAssistan= t Professor of Physical Chemistry 
Current address: Dep= artment of Chemistry,
Faculty of Basic Sciences,University of
=0A
Maragheh, Iran.
E-mail 1: m_esrafili*yahoo.com <= br>=0AE-mail 2: esrafili*maragheh.ac.ir
---------------------------------------------------------= ---------------------------------------------------------------------
=0A

=0A From: "Darpan Aulakh darpan.aulakh2011-,-gmail.com" <owner-ch= emistry*ccl.n= et>
=0A=0A To: "E= srafili, Mehdi D " <m_esrafili*yahoo.com>
Sent: Saturday, June 2, 2012 3:27 PM
=0A Subject: CCL: How to calculate the EDA<= br>

=0A
Dear All
I want to carry out the energy d= ecomposition analysis (especially to calculate the dispersion component). I= s SAPT the only way?? Can anyone suggest any other windows based software t= o complete the purpose?
=0A       &nb= sp;            =           Thanks in advance.=0A
=0A


=0A


--1018391901-781171275-1338906141=:35106-- From owner-chemistry@ccl.net Tue Jun 5 12:25:01 2012 From: "Sergio Manzetti sergio.manzetti[]gmail.com" To: CCL Subject: CCL: Software to superimpose XRD and optimized structures Message-Id: <-47039-120605110939-31983-i9RZM/+66KUIOqYenAwodQ**server.ccl.net> X-Original-From: "Sergio Manzetti" Content-Type: multipart/alternative; boundary="========GMXBoundary250401338908968378365" Date: Tue, 05 Jun 2012 17:09:28 +0200 MIME-Version: 1.0 Sent to CCL by: "Sergio Manzetti" [sergio.manzetti#,#gmail.com] --========GMXBoundary250401338908968378365 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 8bit Christina, you may want to check out SHAeP http://users.abo.fi/mivainio/shaep/ Sergio ----- Original Message ----- > From: Paolo Tosco paolo.tosco-*-unito.it Sent: 06/05/12 02:35 PM To: Manzetti, Sergio Subject: CCL: Software to superimpose XRD and optimized structures Sent to CCL by: Paolo Tosco [paolo.tosco*_*unito.it] Dear Christina, you may use Open3DALIGN for this purpose, which carries out atom-based superimpositions of 3D structures: http://open3dalign.org OpenBabel (included in the Open3DALIGN distribution) will convert your input files to SDF format, if needed. Cheers, Paolo On 06/05/2012 07:12 AM, Christina Jenifer msc christinamsc]^[gmail.com wrote: > Sent to CCL by: "Christina Jenifer msc" [christinamsc|a|gmail.com] > Dear CClers > > I'm currently exploring computational softwares for Atom-by-atom superimposition of the optimized structures over the X-ray structure. So that I would like to ask for advice if there's any suitable software to superimpose this two structures? Kindly help me in this regard. > > Thanks in advance > > With Regards > Christina> > -- ========================================================== Paolo Tosco, Ph.D. Phone: +39 011 6707680 Department of Drug Science Fax: +39 011 6707687 and Technology Mob: +39 348 5537206 Via Pietro Giuria, 9 10125 Torino, Italy http://open3dalign.org E-mail: paolo.tosco!A!unito.it http://open3dqsar.org ==========================================================http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--========GMXBoundary250401338908968378365 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: quoted-printable Christin= a, you may want to check out
=20
=20 SHAeP
=20
=20 http://users.abo.fi/mivainio/shaep/
=20
=20
=20
=20 Sergio
=20
=20

=20 =C2=A0

=20
=20

=20 ----- = Original Message -----

=20

=20 From: = Paolo Tosco paolo.tosco-*-unito.it

=20

=20 Sent: = 06/05/12 02:35 PM

=20

=20 To: Ma= nzetti, Sergio

=20

=20 Subjec= t: CCL: Software to superimpose XRD and optimized structures<= /p>=20
=20

=20
=20 
=20
Sent to CCL by: Paolo Tosco [paolo.tosco*_*unito.it]=20
Dear Christina,=20

you may use Open3DALIGN for this purpose, which carries out atom-based=20
superimpositions of 3D structures:=20

http://open3dalign.org=20

OpenBabel (included in the Open3DALIGN distribution) will convert your=20
input files to SDF format, if needed.=20

Cheers,=20
Paolo=20


On 06/05/2012 07:12 AM, Christina Jenifer msc christinamsc]^[gmail.com=20
wrote:=20
> Sent to CCL by: "Christina Jenifer msc" [christinamsc|a|gmail.com]=20
> Dear CClers=20
>=20
>             I'm currently exploring computational softwares for Atom-b=
y-atom superimposition of the optimized structures over the X-ray structure=
. So that I would like to ask for advice if there's any suitable software t=
o superimpose this two structures? Kindly help me in this regard.=20
>=20
> Thanks in advance=20
>=20
> With Regards=20
> Christina>=20
>=20


--=20
=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=3D=3D=3D=3D=3D=3D=20
Paolo Tosco, Ph.D.                Phone: +39 011 6707680=20
Department of Drug Science        Fax:   +39 011 6707687=20
and Technology                    Mob:   +39 348 5537206=20
Via Pietro Giuria, 9=20
10125 Torino, Italy=20
                                   http://open3dalign.org=20
E-mail: paolo.tosco!A!unito.it      http://open3dqsar.org=20
=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=3D=3D=3D=3D=3D=3D=20



-=3D This is automatically added to each message by the mailing script =3D-=
=20=20=20=20=20=20=20=20

Subscribe/Unsubscribe:=20=20=20

Job: http://www.ccl.net/jobs=20=20=20=20=20
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=20 =C2=A0

=20
=20   --========GMXBoundary250401338908968378365-- From owner-chemistry@ccl.net Tue Jun 5 12:59:00 2012 From: "Giovanni Finoto Caramori giovanni.caramori++ufsc.br" To: CCL Subject: CCL: How to calculate the EDA Message-Id: <-47040-120604104945-31894-8q6PEwwI/YYSVc51x9NtTQ\a/server.ccl.net> X-Original-From: Giovanni Finoto Caramori Content-Type: multipart/alternative; boundary="=_ce03833124e7b2928f1b0dc6481fcca5" Date: Mon, 04 Jun 2012 11:18:22 -0300 MIME-Version: 1.0 Sent to CCL by: Giovanni Finoto Caramori [giovanni.caramori|,|ufsc.br] --=_ce03833124e7b2928f1b0dc6481fcca5 Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Dear Darpan, You can try Su-Li EDA (J. Chem. Phys. 131, 014102 (2009))as implemented in GAMESS-US (http://www.msg.ameslab.gov/gamess/). Sincerely yours, Giovanni On Sat, 2 Jun 2012 16:27:47 +0530, Darpan Aulakh darpan.aulakh2011-,-gmail.com wrote: > Dear All > I want to carry out the energy decomposition analysis (especially to calculate the dispersion component). Is SAPT the only way?? Can anyone suggest any other windows based software to complete the purpose? > Thanks in advance. -- Giovanni Finoto Caramori PhD Departamento de Química - CFM-UFSC Campus Universitário Trindade - C.P. 476 88040-900 Florianópolis/SC http://www.qmc.ufsc.br/~caramori[1] Phone: ++55(48)3721-6844/6845/6846 Fax: ++55(48)3721-6852 Ramal 239 Mobile: ++55(48)9926-8342 --=_ce03833124e7b2928f1b0dc6481fcca5 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=UTF-8

Dear Darpan,

You can try Su-Li EDA (J. Chem. Phys. 131, 014102 (2009))as implemented = in GAMESS-US (http://www.msg.ameslab.gov/gamess/).

Sincerely yours,

Giovanni

On Sat, 2 Jun 2012 16:27:47 +0530, Darpan Aulakh darpan.aulakh2011-,-gma= il.com wrote:

Dear All
I want to carry out the energy decomposition analysis (esp= ecially to calculate the dispersion component). Is SAPT the only way?? Can = anyone suggest any other windows based software to complete the purpose?            =             &nb= sp;     Thanks in advance.

 

--=20
Giovanni Finoto Caramori PhD
Departamento de Química - CFM-UFSC
Campus Universitário Trindade - C.P. 476
88040-900 Florianópolis/SC
http://www.qmc.ufsc.br/~caramori[1]
Phone: ++55(48)3721-6844/6845/6846
 Fax: ++55(48)3721-6852 Ramal 239
Mobile: ++55(48)9926-8342
--=_ce03833124e7b2928f1b0dc6481fcca5-- From owner-chemistry@ccl.net Tue Jun 5 13:34:00 2012 From: "ABHISHEK SHAHI shahi.abhishek1984(0)gmail.com" To: CCL Subject: CCL:G: ESP maxima and minima values Message-Id: <-47041-120605120712-32599-ICXfp5q6G3DIexKtMdO4OA.:.server.ccl.net> X-Original-From: ABHISHEK SHAHI Content-Type: multipart/alternative; boundary=20cf30334b576855fd04c1bbd78f Date: Tue, 5 Jun 2012 21:36:42 +0530 MIME-Version: 1.0 Sent to CCL by: ABHISHEK SHAHI [shahi.abhishek1984*o*gmail.com] --20cf30334b576855fd04c1bbd78f Content-Type: text/plain; charset=ISO-8859-1 Dear CCL Members I want to calculate the maximum and minimum values of electrostatic potential. Gaussview have facilities to visualize it by color code, not by values. Is there any program or code (freeware or academic) to do the same ? I have .chk, .cube files from gaussian software. Any help will be valuable for me. Thanking you all. *ABHISHEK SHAHI* *Research Scholar Inorganic and Physical Chemistry Indian Institute Of Science Bangalore-12* --20cf30334b576855fd04c1bbd78f Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear CCL Members

I want to calculate the maximum and minimum values = of electrostatic potential. Gaussview have facilities to visualize it by co= lor code, not by values. Is there any program or code (freeware or academic= ) to do the same ? I have .chk, .cube files from gaussian software. Any hel= p will be valuable for me. Thanking you all.



=A0ABHISHEK SHAHI

Research Scholar
Inorga= nic and Physical Chemistry
Indian Institute Of Science
Bangal= ore-12

--20cf30334b576855fd04c1bbd78f-- From owner-chemistry@ccl.net Tue Jun 5 14:09:00 2012 From: "Jim Kress ccl_nospam]![kressworks.com" To: CCL Subject: CCL: classical force fields for metal-organic interaction Message-Id: <-47042-120605110223-24261-OdXi0fTVrHpb3EqcPN3M9w=server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 5 Jun 2012 11:02:09 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam/./kressworks.com] Why don't you use ORCA or (if you are independently wealthy :>} ) Turbomole? Jim > -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com]=[ccl.net > [mailto:owner-chemistry+ccl_nospam==kressworks.com]=[ccl.net] On Behalf > Of Egbert Zojer egbert.zojer*|*tugraz.at > Sent: Monday, June 04, 2012 10:52 AM > To: Kress, Jim > Subject: CCL: classical force fields for metal-organic interaction > > > Sent to CCL by: "Egbert Zojer" [egbert.zojer|,|tugraz.at] Dear CCL members, > > I was wondering, whether there are any improved classical force-fields to > more reliably describe the (mostly van der Waals type) - i.e., non-bonding - > interaction between organic molecules (typically conjugated) and metal > surfaces (typically Au(111)). Currently we are using UFF and would like to test > the reliability of our results. > > Thank you ! > > Egbert ZojerTo > 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 look up the X- > Original-From: line in the mail header.> From owner-chemistry@ccl.net Tue Jun 5 14:44:00 2012 From: "Elaine Meng meng!A!cgl.ucsf.edu" To: CCL Subject: CCL: Software to superimpose XRD and optimized structures Message-Id: <-47043-120605133052-20813-AeO2vSr+ub3ceDB5iqCc2Q(_)server.ccl.net> X-Original-From: "Elaine Meng" Date: Tue, 5 Jun 2012 13:30:50 -0400 Sent to CCL by: "Elaine Meng" [meng:_:cgl.ucsf.edu] Hi Christina, Practically any molecular graphics and analysis software can superimpose proteins. For example, the Chimera program I work on has several options, explained here: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html Chimera is a free download for noncommercial use. http://www.cgl.ucsf.edu/chimera/download.html Also, there are dozens of different web servers that superimpose proteins. Some are listed here: http://www.cgl.ucsf.edu/home/meng/grpmt/structalign.html Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco From owner-chemistry@ccl.net Tue Jun 5 16:26:00 2012 From: "Wilfred Li wilfred*_*ucsd.edu" To: CCL Subject: CCL: Call for Applications: NBCR Summer Institute 2012 Message-Id: <-47044-120605162434-18929-g2n1pCPgswUh7ySaHI1xQg**server.ccl.net> X-Original-From: "Wilfred Li" Date: Tue, 5 Jun 2012 16:24:32 -0400 Sent to CCL by: "Wilfred Li" [wilfred,+,ucsd.edu] Call for Applications NBCR Summer Institute 2012 http://si.nbcr.net The National Biomedical Computation Resource (NBCR) will hold its 7th Summer Institute (SI) on July 30 - Aug 3, 2012, in La Jolla California, on the UC San Diego campus. NBCR SI aims to provide significant training opportunities for members of the biomedical research community in targeted areas of computational multiscale biomedical research: computer aided drug discovery; mesoscale modeling; and computational cardiac electrophysiology and mechanics. Accepted students will participate in in-depth, hands-on training sessions on key NBCR tools that are freely available to the academic community, such as Continuity, MGLTools/AutoDock, APBS, GAMer and CADD. They will have opportunities to work with their own data and analyses in problem solving sessions, and hear talks on new directions under the theme of multiscale computational modeling and simulation. Students are encouraged to present posters to discuss ongoing challenges in their own research and explore new opportunities for collaboration. Five tracks are offered this year: 1. Cardiac Mechanics and Electrophysiology 2. Computer Aided Drug Discovery (CADD) pipeline 3. Molecular Electrostatics and Diffusion 4. Mesoscale Modeling of Cardiac Myocytes 5. Virtual Screening using AutoDock Suite of Tools Limited scholarship support and best poster prize will be awarded to selected participants. Space is limited, and students are encouraged to apply early. Last day to apply: July 15, 2012. Flyer Link: http://www2.nbcr.net/wordpress2/si/download/Flyer-NBCR_2012.pdf From owner-chemistry@ccl.net Tue Jun 5 23:51:00 2012 From: "Jason Rigby jason.rigby-$-monash.edu" To: CCL Subject: CCL: Turbomole MPI memory settings for RI-MP2 optimisation calculations Message-Id: <-47045-120605234622-11295-Sy98B3Vq+Z2Yre6NIXrOWg{}server.ccl.net> X-Original-From: "Jason Rigby" Date: Tue, 5 Jun 2012 23:46:21 -0400 Sent to CCL by: "Jason Rigby" [jason.rigby()monash.edu] Hi All, I'm extremely new to Turbomole and I have a few of questions regarding the $maxcor and $ricore parameters in the control file that dictate maximum memory consumption. 1) Does Turbomole provide a mechanism to approximate optimal values for these parameters in a way similar to "EXETYP=CHECK" in GAMESS? 2) In the case of an MPI run, are these values per core, node, or a global limit amongst all processes over all nodes? 3) Are these values treated differently in SMP runs? If anyone with Turbomole experience can spare a moment to help me out, I'd be very appreciative! Thanks :) Jason