From owner-chemistry@ccl.net Sat Sep 9 12:44:00 2017 From: "Andreas Klamt klamt#cosmologic.de" To: CCL Subject: CCL:G: Gaussian SCRF error "No solvent atoms in DisRep" Message-Id: <-52977-170908211713-2931-TFFOtA69IGbKYDknWEsSPA(0)server.ccl.net> X-Original-From: Andreas Klamt Content-Type: multipart/alternative; boundary="------------912F2FD69E6526350F120A24" Date: Sat, 9 Sep 2017 03:16:51 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt!=!cosmologic.de] This is a multi-part message in MIME format. --------------912F2FD69E6526350F120A24 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit For the differences of IEFPCM and CPCM see Comprehensive Comparison of the IEFPCM and SS(V)PE Continuum Solvation Methods with the COSMO Approach http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00601?src=recsys&journalCode=jctcce They are indeed essentially identical. Hence I do not really understand why the more complicated IEFPCM is so much in use. Andreas Am 08.09.2017 um 21:59 schrieb Lufeng Zou g09gv5_+_gmail.com: > Hello Igors, > > One thing to add is that SMD is a solvation model (IEFPCM using SMD > radii for electrostatic part, plus nonelectrostatic terms), so please > do not combine SMD with other solvation models. The program should > have recognized this error and abort, thank you for catching the bug. > > As for the cost, please rest assured that difference between IEFPCM > and CPCM will be minor for most calculations. The only exception is > that for very large molecules with hundreds of atoms, more MEMORY > (RAM) is required for IEFPCM than CPCM. > > Lufeng Zou, Ph.D. > Technical Support > Gaussian, Inc. > help . gaussian.com > > On Thu, Sep 7, 2017 at 10:14 AM, Igors Mihailovs igorsm|a|cfi.lu.lv > > wrote: > > Hi Zhiqiang, > > Yes, I got that, but notice Dr. Zou writes about *G03* PCM models. > It definitely means Gaussian, Inc. people are considering manual > definition of Dis Rep Cav as something truly outdated, so that > they did not update the list for G09 and G16. Whereas both > epsilons and SMD parameters are there for all solvents listed in > the manual. > > So we can probably look for the list of changes between G03 and > G09 to check if the solvent we need has these parameters defined. > In G03 Reference, only 24 solvents are listed as parametrized ones > (neither DMFA, nor AcOH is there), whereas in G09 Reference there > are 184 ones, with those 24 going as first. I consider therefore > that all those 160 solvents cannot be used with Dis Rep Cav… I > checked for CarbonDiSulfide and NitroBenzene – they both produce > the same error, *No solvent atoms in DisRep*. > Some of these solvents quite obviously are not augmentable with > non-electrostatics (e.g., Xylene-mixture), though :) > > With best wishes, > Igors Mihailovs > ISSP UL > > On 06/09/17 23:45, Zhiqiang Zhang zqzhang2101-$-gmail.com > wrote: >> >> Hi Igors, >> >> >> >> Thank you for sharing this comment. In my understanding, the >> comment from Gaussian, Inc. staff means not all the solvents >> available in their database (like n,n-DiMethylFormamide in your >> case) are defined for “Dis Rep Cav” calculation. This is >> information is not very clear in the G09 manual on their website. >> Maybe this is an obsolete method as you mentioned and we can use >> SMD to get the results. >> >> >> >> Best, >> >> Zhiqiang Zhang >> >> >> >> *From: *Igors Mihailovs igorsm^^^cfi.lu.lv >> >> *Sent: *Wednesday, September 6, 2017 12:07 PM >> *To: *Zhang, Zhiqiang >> *Subject: *CCL:G: Gaussian SCRF error "No solvent atoms in DisRep" >> >> >> >> Dear all, >> >> I got the answer from /Gaussian, Inc./, and it is below. >> >> Hello Igors, >> Thank you for giving us a chance to comment. >> >> The problem is that you have "Dis Rep Cav", which are >> non-electrostatic terms included in the G03 PCM models for >> the final energy. However, only limited number of solvents >> are defined (as in G03) and limited number of elements are >> available. For example, n,n-DiMethylFormamide is not >> available in G03. >> >> Please remove "Dis Rep Cav" and it should be fine. >> >> Lufeng Zou, Ph.D. >> >> Technical Support >> >> Gaussian, Inc. >> >> help,,gaussian.com >> >> If we read between the lines, this probably means "please use >> *SMD* and not obsolete methods, if You care about >> non-electrostatic interactions". >> For me, the reason to use Dis Rep Cavwas so that I can use the >> low-cost CPCM instead of presumably high-cost IEFPCM mentioned as >> the basis for SMD in /G09 Reference/ (these considerations were >> based on previous experience by the senior lab staff). However, I >> did not manage to note that "SMD" is in fact "an option to PCM >> calculations", so now I did /p/-nitroaniline in DCM solution with >> SCRF=(CPCM,SMD,Solvent=…), as well as with >> SCRF=(IEFPCM,SMD,Solvent=…), with the following results: >> 1. Both route sections did not bring about any errors >> 2. IEFPCM calculation actually lasted almost a minute less than >> CPCM one (2:7 vs. 2:53 minutes). >> 3. Error on polarization charges was 0.016 for IEFPCM and 0.306 >> for CPCM. >> >> So now I at least understand why CPCM is not suggested by >> /Gaussian, Inc./ staff. Thanks to Dr. Zou for the comment and to >> Zhiqiang Zhang for raising the issue! >> >> With best regards, >> Igors Mihailovs >> ISSP UL >> >> On 03/09/17 19:16, Igors Mihailovs igorsm|*|cfi.lu.lv >> wrote: >> >> Dear all, >> >> >> I have encountered the same problem when trying to use >> DMFAwith SCRF=Read(in my case, also Dis Rep, along with >> Cavand Surface=SAS). Also /Gaussian 09/, rev. D.01. It seems >> to me that N,N-DMFA is not completely defined in this >> version? I postponed writing to /Gaussian, Inc./, but I will >> do it now as other people have the same issue, if nobody >> reports here today. >> >> Using the following non-standard input for PCM: >> Surface=SAS Dis Rep Cav NonEq=Write RSolv=2.647 >> --- end of non-standard input. >> ------------------------------------------------------------------------------ >> Polarizable Continuum Model (PCM) >> ================================= >> Model : C-PCM. >> Atomic radii : UFF (Universal Force Field). >> Polarization charges : Total charges. >> Charge compensation : None. >> Solution method : On-the-fly selection. >> Cavity type : SAS (Solvent Accessible Surface) >> (Alpha=1.000). >> Cavity algorithm : GePol (No added spheres) >> Default sphere list used, NSphG= 52. >> Lebedev-Laikov grids with approx. >> 5.0 points / Ang**2. >> Smoothing algorithm: Karplus/York >> (Gamma=1.0000). >> Polarization charges: spherical >> gaussians, with >> point-specific >> exponents (IZeta= 3). >> Self-potential: point-specific >> (ISelfS= 7). >> Self-field : sphere-specific E.n >> sum rule (ISelfD= 2). >> Solvent : n,n-DiMethylFormamide, Eps= >> 37.219000 Eps(inf)= 2.046330 >> RSolv= 2.647000 Ang. >> ------------------------------------------------------------------------------ >> Warning! Inconsistent VMol and RSolv for this solvent, using >> VMol= 77.69 Ang**3. >> No solvent atoms in DisRep. >> Error termination via Lnk1e in /home/igors/g09/l301.exe at >> Wed May 24 20:48:59 2017. >> Job cpu time: 0 days 0 hours 0 minutes 8.5 seconds. >> File lengths (MBytes): RWF= 610 Int= 0 D2E= 0 >> Chk= 25 Scr= 1 >> >> If there is no manual definitionof RSolv, the following is >> printed: >> >> Solvent : n,n-DiMethylFormamide, Eps= 37.219000 >> Eps(inf)= 2.046330 >> RSolv= 0.000000 Ang. >> ------------------------------------------------------------------------------ >> Warning! Inconsistent VMol and RSolv for this solvent, using >> VMol= 0.00 Ang**3. >> No solvent atoms in DisRep. >> Error termination via Lnk1e in /home/igors/g09/l301.exe at >> Fri May 19 02:16:27 2017 >> >> With best regards, >> Igors Mihailovs >> ISSP UL >> >> On 03/09/17 01:37, Zhiqiang Zhang zhangzq/./udel.edu >> wrote: >> >> Sent to CCL by: "Zhiqiang Zhang" [zhangzq{=}udel.edu ] >> >> Hi all, >> >> I am doing calculation with solvent and get the error "No solvent atoms in DisRep" at the end. I am trying >> >> to include the dispersion and repulsion correction in my calculation. >> >> My input file: >> >> >> >> # opt() freq m062x/6-311G(2df,p) SCRF(CPCM, solvent=AceticAcid, read) >> >> >> >> Title Card Required >> >> >> >> 0 1 >> >> O 0.00000000 0.00000000 0.11813800 >> >> H 0.00000000 0.75681000 -0.47255200 >> >> H 0.00000000 -0.75681000 -0.47255200 >> >> >> >> dis >> >> rep >> >> cav >> >> >> >> /*End of my input file*/ >> >> The last two lines of the log files: >> >> No solvent atoms in DisRep. >> >> Error termination via Lnk1e in /opt/shared/gaussian/g09d01/g09/l301.exe at Sat Sep 2 17:24:24 2017. >> >> >> >> Does anybody know how to resolve this issue? >> >> >> >> >> >> ------------------------------------------------------------------------ >> Avast logo >> >> This email has been checked for viruses by Avast antivirus >> software. www.avast.com >> >> <#m_3808432364363391079_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > -- Ar cieņu, Igors Mihailovs Organisko materiālu laboratorija LU CFI > -- -------------------------------------------------- Prof. Dr. Andreas Klamt CEO / Geschäftsführer COSMOlogic GmbH & Co. KG Imbacher Weg 46 D-51379 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt*cosmologic.de web www.cosmologic.de [University address: Inst. of Physical and Theoretical Chemistry, University of Regensburg] HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt --------------912F2FD69E6526350F120A24 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 8bit
For the differences of IEFPCM and CPCM see
 Comprehensive Comparison of the IEFPCM and SS(V)PE Continuum Solvation Methods with the COSMO Approach
http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00601?src=recsys&journalCode=jctcce

They are indeed essentially identical. Hence I do not really understand why the more complicated IEFPCM is so much in use.

Andreas

Am 08.09.2017 um 21:59 schrieb Lufeng Zou g09gv5_+_gmail.com:
Hello Igors,

One thing to add is that SMD is a solvation model (IEFPCM using SMD radii for electrostatic part, plus nonelectrostatic terms), so please do not combine SMD with other solvation models. The program should have recognized this error and abort, thank you for catching the bug.

As for the cost, please rest assured that difference between IEFPCM and CPCM will be minor for most calculations. The only exception is that for very large molecules with hundreds of atoms, more MEMORY (RAM) is required for IEFPCM than CPCM.

Lufeng Zou, Ph.D.
Technical Support
Gaussian, Inc.
help . gaussian.com

On Thu, Sep 7, 2017 at 10:14 AM, Igors Mihailovs igorsm|a|cfi.lu.lv <owner-chemistry . ccl.net> wrote:
Hi Zhiqiang,

Yes, I got that, but notice Dr. Zou writes about G03 PCM models. It definitely means Gaussian, Inc. people are considering manual definition of Dis Rep Cav as something truly outdated, so that they did not update the list for G09 and G16. Whereas both epsilons and SMD parameters are there for all solvents listed in the manual.

So we can probably look for the list of changes between G03 and G09 to check if the solvent we need has these parameters defined. In G03 Reference, only 24 solvents are listed as parametrized ones (neither DMFA, nor AcOH is there), whereas in G09 Reference there are 184 ones, with those 24 going as first. I consider therefore that all those 160 solvents cannot be used with Dis Rep Cav… I checked for CarbonDiSulfide and NitroBenzene – they both produce the same error, No solvent atoms in DisRep.
Some of these solvents quite obviously are not augmentable with non-electrostatics (e.g., Xylene-mixture), though :)

With best wishes,
Igors Mihailovs
ISSP UL
On 06/09/17 23:45, Zhiqiang Zhang zqzhang2101-$-gmail.com wrote:

Hi Igors,

 

Thank you for sharing this comment. In my understanding, the comment from Gaussian, Inc. staff means not all the solvents available in their database (like n,n-DiMethylFormamide in your case) are defined for “Dis Rep Cav” calculation. This is information is not very clear in the G09 manual on their website. Maybe this is an obsolete method as you mentioned and we can use SMD to get the results.

 

Best,

Zhiqiang  Zhang

 

From: Igors Mihailovs igorsm^^^cfi.lu.lv
Sent: Wednesday, September 6, 2017 12:07 PM
To: Zhang, Zhiqiang
Subject: CCL:G: Gaussian SCRF error "No solvent atoms in DisRep"

 

Dear all,

I got the answer from Gaussian, Inc., and it is below.

Hello Igors,
Thank you for giving us a chance to comment.

The problem is that you have "Dis Rep Cav", which are non-electrostatic terms included in the G03 PCM models for the final energy. However, only limited number of solvents are defined (as in G03) and limited number of elements are available. For example, n,n-DiMethylFormamide is not available in G03.

Please remove "Dis Rep Cav" and it should be fine.

Lufeng Zou, Ph.D.
Technical Support
Gaussian, Inc.
help,,gaussian.com

If we read between the lines, this probably means "please use SMD and not obsolete methods, if You care about non-electrostatic interactions".
For me, the reason to use Dis Rep Cav was so that I can use the low-cost CPCM instead of presumably high-cost IEFPCM mentioned as the basis for SMD in G09 Reference (these considerations were based on previous experience by the senior lab staff). However, I did not manage to note that "SMD" is in fact "an option to PCM calculations", so now I did p-nitroaniline in DCM solution with SCRF=(CPCM,SMD,Solvent=…), as well as with SCRF=(IEFPCM,SMD,Solvent=…), with the following results:
1. Both route sections did not bring about any errors
2. IEFPCM calculation actually lasted almost a minute less than CPCM one (2:7 vs. 2:53 minutes).
3. Error on polarization charges was 0.016 for IEFPCM and 0.306 for CPCM.

So now I at least understand why CPCM is not suggested by Gaussian, Inc. staff. Thanks to Dr. Zou for the comment and to
Zhiqiang Zhang for raising the issue!

With best regards,
Igors Mihailovs
ISSP UL

On 03/09/17 19:16, Igors Mihailovs igorsm|*|cfi.lu.lv wrote:

Dear all,


I have encountered the same problem when trying to use DMFA with SCRF=Read (in my case, also Dis Rep, along with Cav and Surface=SAS). Also Gaussian 09, rev. D.01. It seems to me that N,N-DMFA is not completely defined in this version? I postponed writing to Gaussian, Inc., but I will do it now as other people have the same issue, if nobody reports here today.

Using the following non-standard input for PCM:
 Surface=SAS Dis Rep Cav NonEq=Write RSolv=2.647
 --- end of non-standard input.
 ------------------------------------------------------------------------------
 Polarizable Continuum Model (PCM)
 =================================
 Model                : C-PCM.
 Atomic radii         : UFF (Universal Force Field).
 Polarization charges : Total charges.
 Charge compensation  : None.
 Solution method      : On-the-fly selection.
 Cavity type          : SAS (Solvent Accessible Surface) (Alpha=1.000).
 Cavity algorithm     : GePol (No added spheres)
                        Default sphere list used, NSphG=   52.
                        Lebedev-Laikov grids with approx.  5.0 points / Ang**2.
                        Smoothing algorithm: Karplus/York (Gamma=1.0000).
                        Polarization charges: spherical gaussians, with
                                              point-specific exponents (IZeta= 3).
                        Self-potential: point-specific (ISelfS= 7).
                        Self-field    : sphere-specific E.n sum rule (ISelfD= 2).
 Solvent              : n,n-DiMethylFormamide, Eps=  37.219000 Eps(inf)=   2.046330
                        RSolv=   2.647000 Ang.
 ------------------------------------------------------------------------------
 Warning! Inconsistent VMol and RSolv for this solvent, using VMol=   77.69 Ang**3.
 No solvent atoms in DisRep.
 Error termination via Lnk1e in /home/igors/g09/l301.exe at Wed May 24 20:48:59 2017.
 Job cpu time:       0 days  0 hours  0 minutes  8.5 seconds.
 File lengths (MBytes):  RWF=    610 Int=      0 D2E=      0 Chk=     25 Scr=      1

If there is no manual definition of RSolv, the following is printed:

Solvent              : n,n-DiMethylFormamide, Eps=  37.219000 Eps(inf)=   2.046330
                        RSolv=   0.000000 Ang.
 ------------------------------------------------------------------------------
 Warning! Inconsistent VMol and RSolv for this solvent, using VMol=    0.00 Ang**3.
 No solvent atoms in DisRep.
 Error termination via Lnk1e in /home/igors/g09/l301.exe at Fri May 19 02:16:27 2017

With best regards,
Igors Mihailovs
ISSP UL

On 03/09/17 01:37, Zhiqiang Zhang zhangzq/./udel.edu wrote:

Sent to CCL by: "Zhiqiang  Zhang" [zhangzq{=}udel.edu]
Hi all,
I am doing calculation with solvent and get the error "No solvent atoms in DisRep" at the end. I am trying 
to include the dispersion and repulsion correction in my calculation.
My input file:
 
# opt() freq m062x/6-311G(2df,p) SCRF(CPCM, solvent=AceticAcid, read)
 
Title Card Required
 
0 1
 O                  0.00000000    0.00000000    0.11813800
 H                  0.00000000    0.75681000   -0.47255200
 H                  0.00000000   -0.75681000   -0.47255200
 
dis
rep
cav
 
/*End of my input file*/
The last two lines of the log files:
No solvent atoms in DisRep.
 Error termination via Lnk1e in /opt/shared/gaussian/g09d01/g09/l301.exe at Sat Sep  2 17:24:24 2017.
 
Does anybody know how to resolve this issue?
 

 

Avast logo

This email has been checked for viruses by Avast antivirus software. www.avast.com

-- Ar cieņu, Igors Mihailovs Organisko materiālu laboratorija LU CFI

-- 
--------------------------------------------------

Prof. Dr. Andreas Klamt
CEO / Geschäftsführer
COSMOlogic GmbH & Co. KG
Imbacher Weg 46
D-51379 Leverkusen, Germany

phone  	+49-2171-731681
fax    	+49-2171-731689
e-mail 	klamt*cosmologic.de
web    	www.cosmologic.de

[University address:      Inst. of Physical and
Theoretical Chemistry, University of Regensburg]

HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH
HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt
--------------912F2FD69E6526350F120A24-- From owner-chemistry@ccl.net Sat Sep 9 16:49:00 2017 From: "Igors Mihailovs igorsm###cfi.lu.lv" To: CCL Subject: CCL:G: Gaussian SCRF error "No solvent atoms in DisRep" Message-Id: <-52978-170909152208-9608-h/CxNDci0v+XlZe2X8CVug-$-server.ccl.net> X-Original-From: Igors Mihailovs Content-Language: en-US Content-Type: multipart/alternative; boundary="------------483F4A9C5BCDD4C4CD10DAA4" Date: Sat, 9 Sep 2017 22:24:27 +0300 MIME-Version: 1.0 Sent to CCL by: Igors Mihailovs [igorsm===cfi.lu.lv] This is a multi-part message in MIME format. --------------483F4A9C5BCDD4C4CD10DAA4 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit Dear Dr. Zou, Thank You for the further clarification! One another thing I am a little curious about -- only in CPCM+SMD calculation the escaped charge is /reported/ (in my case, enormous 0.46984). Is that because of some threshold for things to appear in output, or due to a different algorithm in use (for IEFPCM, even with #P there is no sign of escaped charge)? Dear Dr. Klamt, That's why I was surprised by the results I had got, because I have read before, well, at least the abstract of the article You cited (due to the lack of access) /and/ Your article of 2011 (DOI: 10.1002/wcms.56 ) where You argued that, although it was proven that the best value of /x/ in the equation for COSMO is 0.5, "[u]nfortunately, several reimplementations of COSMO, including C-PCM, set the value of /x/ to zero either by default or fixed." Can this be the reason? Or is it simply because SMD model in Gaussian is optimized for IEFPCM, not CPCM?(Maybe Dr. Zou can comment on that.) You also mention that "in the literature the COSMO approximation is often claimed to be applicable only to polar solvents, it needs to be emphasized that for neutral compounds the COSMO approximation with x = 0.5 provides very accurate results down to ε = 2". Maybe this is why COSMO is not that popular? On the other hand, if, as Dr. Zou said, the differences in computational cost arise only in really large molecules, maybe software developers just feel it is not that urgent to implement COSMO if they already have another methods implemented… By "the equation" I mean the equation of COSMO scaling factor for unscreened charge density, /f/ (/ε/) = (/ε/ – 1) / (/ε/ + /x/) --------------------------------------------------------------------------- To mention some other details, the differing part in the output is the following: ***** CPCM_SMD.out No special actions if energy rises. Using charges instead of weights in PCMQM. Inv3: Mode=1 IEnd= 5838075. Iteration 1 A*A^-1 deviation from unit magnitude is 2.78D-15 for 865. Iteration 1 A*A^-1 deviation from orthogonality is 1.65D-15 for 711 187. Iteration 1 A^-1*A deviation from unit magnitude is 3.11D-15 for 813. Iteration 1 A^-1*A deviation from orthogonality is 1.65D-15 for 1142 64. Escaped charge = 0.46984 Error on total polarization charges = 0.30616 SCF Done: E(RB3LYP) = -492.141763479 A.U. after 13 cycles NFock= 13 Conv=0.34D-08 -V/T= 2.0086 SMD-CDS (non-electrostatic) energy (kcal/mol) = -1.55 ***** IEFPCM_SMD.OUT No special actions if energy rises. Inv3: Mode=1 IEnd= 5838075. Iteration 1 A*A^-1 deviation from unit magnitude is 3.55D-15 for 317. Iteration 1 A*A^-1 deviation from orthogonality is 2.67D-15 for 629 474. Iteration 1 A^-1*A deviation from unit magnitude is 3.33D-15 for 317. Iteration 1 A^-1*A deviation from orthogonality is 2.19D-15 for 545 224. Error on total polarization charges = 0.01601 SCF Done: E(RB3LYP) = -492.138961313 A.U. after 13 cycles NFock= 13 Conv=0.35D-08 -V/T= 2.0086 SMD-CDS (non-electrostatic) energy (kcal/mol) = -1.55 Yours sincerely, Igors Mihailovs ISSP UL On 08/09/17 22:59, Lufeng Zou g09gv5_+_gmail.com wrote: > Hello Igors, > > One thing to add is that SMD is a solvation model (IEFPCM using SMD > radii for electrostatic part, plus nonelectrostatic terms), so please > do not combine SMD with other solvation models. The program should > have recognized this error and abort, thank you for catching the bug. > > As for the cost, please rest assured that difference between IEFPCM > and CPCM will be minor for most calculations. The only exception is > that for very large molecules with hundreds of atoms, more MEMORY > (RAM) is required for IEFPCM than CPCM. > > Lufeng Zou, Ph.D. > Technical Support > Gaussian, Inc. > help . gaussian.com On 09/09/17 04:16, Andreas Klamt klamt#cosmologic.de wrote: > For the differences of IEFPCM and CPCM see > Comprehensive Comparison of the IEFPCM and SS(V)PE Continuum > Solvation Methods with the COSMO Approach > http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00601?src=recsys&journalCode=jctcce > > They are indeed essentially identical. Hence I do not really > understand why the more complicated IEFPCM is so much in use. > > Andreas --------------483F4A9C5BCDD4C4CD10DAA4 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit Dear Dr. Zou,

Thank You for the further clarification!

One another thing I am a little curious about -- only in CPCM+SMD calculation the escaped charge is reported (in my case, enormous 0.46984). Is that because of some threshold for things to appear in output, or due to a different algorithm in use (for IEFPCM, even with #P there is no sign of escaped charge)?

Dear Dr. Klamt,

That's why I was surprised by the results I had got, because I have read before, well, at least the abstract of the article You cited (due to the lack of access) and Your article of 2011 (DOI: 10.1002/wcms.56) where You argued that, although it was proven that the best value of x in the equation for COSMO is 0.5, "[u]nfortunately, several reimplementations of COSMO, including C-PCM, set the value of x to zero either by default or fixed." Can this be the reason? Or is it simply because SMD model in Gaussian is optimized for IEFPCM, not CPCM? (Maybe Dr. Zou can comment on that.)
You also mention that "in the literature the COSMO approximation is often claimed to be applicable only to polar solvents, it needs to be emphasized that for neutral compounds the COSMO approximation with x = 0.5 provides very accurate results down to ε = 2". Maybe this is why COSMO is not that popular? On the other hand, if, as Dr. Zou said, the differences in computational cost arise only in really large molecules, maybe software developers just feel it is not that urgent to implement COSMO if they already have another methods implemented…

By "the equation" I mean the equation of COSMO scaling factor for unscreened charge density,

f (ε) = (ε – 1) / (ε + x)

---------------------------------------------------------------------------

To mention some other details, the differing part in the output is the following:

***** CPCM_SMD.out
 No special actions if energy rises.
 Using charges instead of weights in PCMQM.
 Inv3:  Mode=1 IEnd=     5838075.
 Iteration    1 A*A^-1 deviation from unit magnitude is 2.78D-15 for    865.
 Iteration    1 A*A^-1 deviation from orthogonality  is 1.65D-15 for    711    187.
 Iteration    1 A^-1*A deviation from unit magnitude is 3.11D-15 for    813.
 Iteration    1 A^-1*A deviation from orthogonality  is 1.65D-15 for   1142     64.
 Escaped charge =  0.46984
 Error on total polarization charges =  0.30616
 SCF Done:  E(RB3LYP) =  -492.141763479     A.U. after   13 cycles
            NFock= 13  Conv=0.34D-08     -V/T= 2.0086
 SMD-CDS (non-electrostatic) energy       (kcal/mol) =      -1.55

***** IEFPCM_SMD.OUT
 No special actions if energy rises.
 Inv3:  Mode=1 IEnd=     5838075.
 Iteration    1 A*A^-1 deviation from unit magnitude is 3.55D-15 for    317.
 Iteration    1 A*A^-1 deviation from orthogonality  is 2.67D-15 for    629    474.
 Iteration    1 A^-1*A deviation from unit magnitude is 3.33D-15 for    317.
 Iteration    1 A^-1*A deviation from orthogonality  is 2.19D-15 for    545    224.
 Error on total polarization charges =  0.01601
 SCF Done:  E(RB3LYP) =  -492.138961313     A.U. after   13 cycles
            NFock= 13  Conv=0.35D-08     -V/T= 2.0086
 SMD-CDS (non-electrostatic) energy       (kcal/mol) =      -1.55


Yours sincerely,
Igors Mihailovs
ISSP UL

On 08/09/17 22:59, Lufeng Zou g09gv5_+_gmail.com wrote:
Hello Igors,

One thing to add is that SMD is a solvation model (IEFPCM using SMD radii for electrostatic part, plus nonelectrostatic terms), so please do not combine SMD with other solvation models. The program should have recognized this error and abort, thank you for catching the bug.

As for the cost, please rest assured that difference between IEFPCM and CPCM will be minor for most calculations. The only exception is that for very large molecules with hundreds of atoms, more MEMORY (RAM) is required for IEFPCM than CPCM.

Lufeng Zou, Ph.D.
Technical Support
Gaussian, Inc.
help . gaussian.com


On 09/09/17 04:16, Andreas Klamt klamt#cosmologic.de wrote:
For the differences of IEFPCM and CPCM see
 Comprehensive Comparison of the IEFPCM and SS(V)PE Continuum Solvation Methods with the COSMO Approach
http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00601?src=recsys&journalCode=jctcce

They are indeed essentially identical. Hence I do not really understand why the more complicated IEFPCM is so much in use.

Andreas
--------------483F4A9C5BCDD4C4CD10DAA4-- From owner-chemistry@ccl.net Sat Sep 9 17:24:00 2017 From: "Zachary B Smithline zachary.smithline(0)yale.edu" To: CCL Subject: CCL: AM1-BCC charges in Antechamber Message-Id: <-52979-170909170321-19290-h8mbCBi05dXyRE0IVz8z9g-$-server.ccl.net> X-Original-From: "Zachary B Smithline" Date: Sat, 9 Sep 2017 17:03:19 -0400 Sent to CCL by: "Zachary B Smithline" [zachary.smithline]_[yale.edu] Dear All, Does anybody have a lot of experience deriving AM1-BCC charges quickly in Antechamber? I am trying to parameterize charges for: 3' adenine nucleotide with its 3'O deprotonated (since the 3' terminal residues in Amber usually have -0.6921 charge, my residue should have -1.6921); pyrophosphate (charge -4); and dATP (charge -4). After generating .pdbs, I was trying to run the command: antechamber -i FILE_NAME.pdb -fi pdb -o FILE_NAME.mol2 -fo mol2 -c bcc -s 2 -nc CHARGE Both dATP and pyrophosphate give me errors when I use -nc -4; however, when I decrease the charge (say, to -2), the antechamber command works. Is it ok to assume the charge distributes uniformly as it is decreased, meaning: can I just double all my charges? For the 3' adenine nucleotide with its 3'O deprotonated, I don't think antechamber will take a non-integer charge. Can I use the same strategy, and just scale the charges? If not, does anybody have a suggestion as to how to deal with these problems? Is there any simple way to do these tasks in Antechamber? Many thanks, Zach Smithline Lab of Thomas Steitz Departments of MB&B and Chemistry Yale University From owner-chemistry@ccl.net Sat Sep 9 22:46:00 2017 From: "Jim Kress jimkress35:gmail.com" To: CCL Subject: CCL: AM1-BCC charges in Antechamber Message-Id: <-52980-170909224424-5543-sbJJxPxZM4NL584iqnWrsw-.-server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Sat, 9 Sep 2017 22:44:03 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [jimkress35~!~gmail.com] Did you ask your question on the Amber mailing list? I see these questions coming up quite frequently there. AMBER mailing list AMBER|*|ambermd.org http://lists.ambermd.org/mailman/listinfo/amber Jim -----Original Message----- > From: owner-chemistry+jimkress35==gmail.com|*|ccl.net [mailto:owner-chemistry+jimkress35==gmail.com|*|ccl.net] On Behalf Of Zachary B Smithline zachary.smithline(0)yale.edu Sent: Saturday, September 09, 2017 5:03 PM To: Kress, Jim Subject: CCL: AM1-BCC charges in Antechamber Sent to CCL by: "Zachary B Smithline" [zachary.smithline]_[yale.edu] Dear All, Does anybody have a lot of experience deriving AM1-BCC charges quickly in Antechamber? I am trying to parameterize charges for: 3' adenine nucleotide with its 3'O deprotonated (since the 3' terminal residues in Amber usually have -0.6921 charge, my residue should have -1.6921); pyrophosphate (charge -4); and dATP (charge -4). After generating .pdbs, I was trying to run the command: antechamber -i FILE_NAME.pdb -fi pdb -o FILE_NAME.mol2 -fo mol2 -c bcc -s 2 -nc CHARGE Both dATP and pyrophosphate give me errors when I use -nc -4; however, when I decrease the charge (say, to -2), the antechamber command works. Is it ok to assume the charge distributes uniformly as it is decreased, meaning: can I just double all my charges? For the 3' adenine nucleotide with its 3'O deprotonated, I don't think antechamber will take a non-integer charge. Can I use the same strategy, and just scale the charges? If not, does anybody have a suggestion as to how to deal with these problems? Is there any simple way to do these tasks in Antechamber? Many thanks, Zach Smithline Lab of Thomas Steitz Departments of MB&B and Chemistry Yale Universityhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt