From owner-chemistry@ccl.net Tue Jul 10 10:20:00 2018 From: "Jorge Iulek iulek]~[uepg.br" <owner-chemistry\a/server.ccl.net> To: CCL Subject: CCL: get electrostatic potential at atoms and molecular polarizability Message-Id: <-53384-180710083859-3780-CEMaGiXyV9i/lY0wCymHiQ\a/server.ccl.net> X-Original-From: Jorge Iulek <iulek|*|uepg.br> Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Tue, 10 Jul 2018 09:38:45 -0300 MIME-Version: 1.0 Sent to CCL by: Jorge Iulek [iulek(~)uepg.br] Dear all, I have some molecules structurally similar to ones that were used in a previous (not by me) QSAR study. To these, a model (equation to estimate biological activity) was proposed (very good correlation) to explain (reasonably well) activities based on QM descriptors. Therefore I want to check what the biological activity is estimated for my similar molecules. I need to calculate the electrostatic potential (EP) at two specific atoms and the molecule polarizability, to make the prediction. I should say that the model was established using other QM program, nevertheless, but I must go for the free academic program gamess. The article states that the molecules were structure optimized (3D gemometry) using DFT theory, the 6-31G(d) basis set at the hybrid functional B3LYP. My gamess input for optimization contains: ------------------------ $contrl dfttyp=B3LYP runtyp=optimize nzvar=72 coord=zmt icharg=0 $end $system timlim=525600.0 MWORDS=6 $end $statpt hess=guess nstep=100 nprt=-1 npun=0 $end $basis GBASIS=N31 NGAUSS=6 NDFUNC=1 $end $guess guess=huckel $end $SCF DIRSCF=.true. CONV=1d-7 FDIFF=.FALSE. $end $DFT DFTTYP=B3LYP $end ... here comes coordinates (as zmatrix), etc... --------------------------- And then from the resulting .dat file I extract both $DATA and $VEC lines to input with lines below to calculate EP... ---------------- $contrl runtyp=prop dfttyp=B3LYP nzvar=0 coord=unique icharg=0 $end $system timlim=525600.0 MWORDS=6 $end $basis GBASIS=N31 NGAUSS=6 NDFUNC=1 $end $guess guess=moread $end $DFT DFTTYP=B3LYP $end $ELPOT IEPOT=1 WHERE=NUCLEI OUTPUT=BOTH $end $FFCALC OFFDIA=.TRUE. $end ... $DATA and $VEC ... ------- And molecular polarizability with... -------------- $contrl runtyp=energy local=boys $end $local poldcm=.true. polnum=.true. fcore=.false. $end $contrl dfttyp=B3LYP nzvar=0 coord=unique icharg=0 $end $SYSTEM MWORDS=6 $END $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 $END $GUESS GUESS=moread $END $SCF DIRSCF=.true. CONV=1d-7 FDIFF=.FALSE. $end $DFT DFTTYP=B3LYP $end ... $DATA and $VEC ... ------------ The matter is that with these instructions, even for the original molecules (of the QSAR study), I cannot reproduce author's results. In fact, the QSAR model (equation) seems to be quite sensitive to the resulting EP (their coefficients in the equation are large, so minor differences have large impact). Therefore, possibly I miss something here at my input files for gamess. I would much thank if someone would criticize my inputs and point to some error. Should I expect, in any case, to get very approximate results, once the calculation implies the same theory, basis set, functional, etc. (I guess), at using different QM programs? Yours, Jorge From owner-chemistry@ccl.net Tue Jul 10 11:53:01 2018 From: "Grzegorz Mazur mazur ~~ chemia.uj.edu.pl" <owner-chemistry**server.ccl.net> To: CCL Subject: CCL: get electrostatic potential at atoms and molecular polarizability Message-Id: <-53385-180710115105-30354-pxGZmF0KtZr43cKDWa0zYQ**server.ccl.net> X-Original-From: Grzegorz Mazur <mazur%%chemia.uj.edu.pl> Content-Transfer-Encoding: base64 Content-Type: text/html; charset=utf-8 Date: Tue, 10 Jul 2018 17:50:47 +0200 MIME-Version: 1.0 Sent to CCL by: Grzegorz Mazur [mazur%chemia.uj.edu.pl] PGRpdiBkaXI9J2F1dG8nPkhpLDxkaXYgZGlyPSJhdXRvIj48YnI+PC9kaXY+PGRpdiBkaXI9ImF1 dG8iPkZpcnN0IG9mIGFsbCwgY2hlY2sgaWYgeW91IHVzZSB0aGUgc2FtZSBCM0xZUCwgb25lIGRl ZmluaXRpb24gdXNlcyBWV04zLCBhbm90aGVyIFZXTjUuIFRoZW4sIGNoZWNrIGlmIHlvdSB1c2Ug dGhlIHNhbWUgYmFzaXMgc2V0IChDYXJ0ZXNpYW4gdnMgc3BoZXJpY2FsIGFrYSA2cCB2cyA1cCku IFRoZXNlIGFyZSB0aGUgbW9zdCBvYnZpb3VzIHN1c3BlY3RzLjwvZGl2PjxkaXYgZGlyPSJhdXRv Ij48YnI+PC9kaXY+PGRpdiBkaXI9ImF1dG8iPlJlZ2FyZHMsPC9kaXY+PGRpdiBkaXI9ImF1dG8i PkdyemVnb3J6IE1henVyPC9kaXY+PC9kaXY+ From owner-chemistry@ccl.net Tue Jul 10 12:42:01 2018 From: "David Shobe shobedavid-,-gmail.com" <owner-chemistry:server.ccl.net> To: CCL Subject: CCL: get electrostatic potential at atoms and molecular polarizability Message-Id: <-53386-180710124023-18963-Uq6U71TQ7s1C2yq6qseqzg:server.ccl.net> X-Original-From: David Shobe <shobedavid%x%gmail.com> Content-Type: multipart/alternative; boundary="00000000000000319b0570a7c96f" Date: Tue, 10 Jul 2018 11:40:08 -0500 MIME-Version: 1.0 Sent to CCL by: David Shobe [shobedavid|-|gmail.com] --00000000000000319b0570a7c96f Content-Type: text/plain; charset="UTF-8" I don't know if this will fix it, but there is the issue of 5d (spherical) v. 6d (Cartesian). You d have to find out what the original researchers used. On Tue, Jul 10, 2018, 11:22 AM Jorge Iulek iulek]~[uepg.br < owner-chemistry-*-ccl.net> wrote: > > Sent to CCL by: Jorge Iulek [iulek(~)uepg.br] > Dear all, > > > I have some molecules structurally similar to ones that were used > in a previous (not by me) QSAR study. To these, a model (equation to > estimate biological activity) was proposed (very good correlation) to > explain (reasonably well) activities based on QM descriptors. Therefore > I want to check what the biological activity is estimated for my similar > molecules. I need to calculate the electrostatic potential (EP) at two > specific atoms and the molecule polarizability, to make the prediction. > I should say that the model was established using other QM program, > nevertheless, but I must go for the free academic program gamess. The > article states that the molecules were structure optimized (3D > gemometry) using DFT theory, the 6-31G(d) basis set at the hybrid > functional B3LYP. > > My gamess input for optimization contains: > ------------------------ > $contrl dfttyp=B3LYP runtyp=optimize nzvar=72 coord=zmt icharg=0 $end > $system timlim=525600.0 MWORDS=6 $end > $statpt hess=guess nstep=100 nprt=-1 npun=0 $end > $basis GBASIS=N31 NGAUSS=6 NDFUNC=1 $end > $guess guess=huckel $end > $SCF DIRSCF=.true. CONV=1d-7 FDIFF=.FALSE. $end > $DFT DFTTYP=B3LYP $end > ... here comes coordinates (as zmatrix), etc... > --------------------------- > > And then from the resulting .dat file I extract both $DATA and $VEC > lines to input with lines below to calculate EP... > ---------------- > $contrl runtyp=prop dfttyp=B3LYP nzvar=0 coord=unique icharg=0 $end > $system timlim=525600.0 MWORDS=6 $end > $basis GBASIS=N31 NGAUSS=6 NDFUNC=1 $end > $guess guess=moread $end > $DFT DFTTYP=B3LYP $end > $ELPOT IEPOT=1 WHERE=NUCLEI OUTPUT=BOTH $end > $FFCALC OFFDIA=.TRUE. $end > ... $DATA and $VEC ... > ------- > > And molecular polarizability with... > -------------- > $contrl runtyp=energy local=boys $end > $local poldcm=.true. polnum=.true. fcore=.false. $end > $contrl dfttyp=B3LYP nzvar=0 coord=unique icharg=0 $end > $SYSTEM MWORDS=6 $END > $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 $END > $GUESS GUESS=moread $END > $SCF DIRSCF=.true. CONV=1d-7 FDIFF=.FALSE. $end > $DFT DFTTYP=B3LYP $end > ... $DATA and $VEC ... > ------------ > > The matter is that with these instructions, even for the original > molecules (of the QSAR study), I cannot reproduce author's results. In > fact, the QSAR model (equation) seems to be quite sensitive to the > resulting EP (their coefficients in the equation are large, so minor > differences have large impact). Therefore, possibly I miss something > here at my input files for gamess. I would much thank if someone would > criticize my inputs and point to some error. Should I expect, in any > case, to get very approximate results, once the calculation implies the > same theory, basis set, functional, etc. (I guess), at using different > QM programs? > > Yours, > > > Jorge> > > --00000000000000319b0570a7c96f Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable <div dir=3D"auto">I don't know if this will fix it, but there is the is= sue of 5d (spherical) v. 6d (Cartesian). You d have to find out what the or= iginal researchers used.<div dir=3D"auto"><br></div></div><br><div class=3D= "gmail_quote"><div dir=3D"ltr">On Tue, Jul 10, 2018, 11:22 AM Jorge Iulek i= ulek]~[<a href=3D"http://uepg.br">uepg.br</a> <<a href=3D"mailto:owner-c= hemistry-*-ccl.net">owner-chemistry-*-ccl.net</a>> wrote:<br></div><blockquo= te class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc so= lid;padding-left:1ex"><br> Sent to CCL by: Jorge Iulek [iulek(~)<a href=3D"http://uepg.br" rel=3D"nore= ferrer noreferrer" target=3D"_blank">uepg.br</a>]<br> Dear all,<br> <br> <br> =C2=A0=C2=A0=C2=A0=C2=A0 I have some molecules structurally similar to ones= that were used <br> in a previous (not by me) QSAR study. To these, a model (equation to <br> estimate biological activity) was proposed (very good correlation) to <br> explain (reasonably well) activities based on QM descriptors. Therefore <br= > I want to check what the biological activity is estimated for my similar <b= r> molecules. I need to calculate the electrostatic potential (EP) at two <br> specific atoms and the molecule polarizability, to make the prediction. <br= > I should say that the model was established using other QM program, <br> nevertheless, but I must go for the free academic program gamess. The <br> article states that the molecules were structure optimized (3D <br> gemometry) using=C2=A0 DFT theory, the 6-31G(d) basis set at the hybrid <br= > functional B3LYP.<br> <br> =C2=A0=C2=A0=C2=A0=C2=A0 My gamess input for optimization contains:<br> ------------------------<br> =C2=A0=C2=A0$contrl dfttyp=3DB3LYP runtyp=3Doptimize nzvar=3D72 coord=3Dzmt= icharg=3D0 $end<br> =C2=A0=C2=A0$system timlim=3D525600.0 MWORDS=3D6 $end<br> =C2=A0=C2=A0$statpt hess=3Dguess nstep=3D100 nprt=3D-1 npun=3D0 $end<br> =C2=A0=C2=A0$basis=C2=A0 GBASIS=3DN31 NGAUSS=3D6 NDFUNC=3D1 $end<br> =C2=A0=C2=A0$guess=C2=A0 guess=3Dhuckel $end<br> =C2=A0=C2=A0$SCF DIRSCF=3D.true. CONV=3D1d-7 FDIFF=3D.FALSE. $end<br> =C2=A0=C2=A0$DFT DFTTYP=3DB3LYP $end<br> ... here comes coordinates (as zmatrix), etc...<br> ---------------------------<br> <br> =C2=A0=C2=A0=C2=A0=C2=A0 And then from the resulting .dat file I extract bo= th $DATA and $VEC <br> lines to input with lines below to calculate EP...<br> ----------------<br> =C2=A0 $contrl runtyp=3Dprop dfttyp=3DB3LYP nzvar=3D0 coord=3Dunique icharg= =3D0 $end<br> =C2=A0 $system timlim=3D525600.0 MWORDS=3D6 $end<br> =C2=A0 $basis=C2=A0 GBASIS=3DN31 NGAUSS=3D6 NDFUNC=3D1 $end<br> =C2=A0 $guess guess=3Dmoread $end<br> =C2=A0 $DFT DFTTYP=3DB3LYP $end<br> =C2=A0 $ELPOT IEPOT=3D1 WHERE=3DNUCLEI OUTPUT=3DBOTH $end<br> =C2=A0 $FFCALC OFFDIA=3D.TRUE. $end<br> ... $DATA and $VEC ...<br> -------<br> <br> =C2=A0=C2=A0=C2=A0=C2=A0 And molecular polarizability with...<br> --------------<br> =C2=A0 $contrl runtyp=3Denergy local=3Dboys $end<br> =C2=A0 $local=C2=A0 poldcm=3D.true. polnum=3D.true.=C2=A0 =C2=A0fcore=3D.fa= lse.=C2=A0 $end<br> =C2=A0 $contrl dfttyp=3DB3LYP nzvar=3D0 coord=3Dunique icharg=3D0 $end<br> =C2=A0 $SYSTEM MWORDS=3D6 $END<br> =C2=A0 $BASIS=C2=A0 GBASIS=3DN31 NGAUSS=3D6 NDFUNC=3D1 $END<br> =C2=A0 $GUESS=C2=A0 GUESS=3Dmoread $END<br> =C2=A0 $SCF DIRSCF=3D.true. CONV=3D1d-7 FDIFF=3D.FALSE. $end<br> =C2=A0 $DFT DFTTYP=3DB3LYP $end<br> ... $DATA and $VEC ...<br> ------------<br> <br> =C2=A0=C2=A0=C2=A0=C2=A0 The matter is that with these instructions, even f= or the original <br> molecules (of the QSAR study), I cannot reproduce author's results. In = <br> fact, the QSAR model (equation) seems to be quite sensitive to the <br> resulting EP (their coefficients in the equation are large, so minor <br> differences have large impact). Therefore, possibly I miss something <br> here at my input files for gamess. I would much thank if someone would <br> criticize my inputs and point to some error. Should I expect, in any <br> case, to get very approximate results, once the calculation implies the <br= > same theory, basis set, functional, etc. (I guess), at using different <br> QM programs?<br> <br> =C2=A0=C2=A0=C2=A0=C2=A0 Yours,<br> <br> <br> Jorge<br> <br> <br> <br> -=3D This is automatically added to each message by the mailing script =3D-= <br<br=<br<br> <br> E-mail to subscribers: <a href=3D"mailto:CHEMISTRY-*-ccl.net" target=3D"_blan= k" rel=3D"noreferrer">CHEMISTRY-*-ccl.net</a> or use:<br> =C2=A0 =C2=A0 =C2=A0 <a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_mes= sage" rel=3D"noreferrer noreferrer" target=3D"_blank">http://www.ccl.net/cg= i-bin/ccl/send_ccl_message</a><br> <br> E-mail to administrators: <a href=3D"mailto:CHEMISTRY-REQUEST-*-ccl.net" targ= et=3D"_blank" rel=3D"noreferrer">CHEMISTRY-REQUEST-*-ccl.net</a> or use<br> =C2=A0 =C2=A0 =C2=A0 <a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_mes= sage" rel=3D"noreferrer noreferrer" target=3D"_blank">http://www.ccl.net/cg= i-bin/ccl/send_ccl_message</a><br> <br<br> =C2=A0 =C2=A0 =C2=A0 <a href=3D"http://www.ccl.net/chemistry/sub_unsub.shtm= l" rel=3D"noreferrer noreferrer" target=3D"_blank">http://www.ccl.net/chemi= stry/sub_unsub.shtml</a><br> <br> Before posting, check wait time at: <a href=3D"http://www.ccl.net" rel=3D"n= oreferrer noreferrer" target=3D"_blank">http://www.ccl.net</a><br> <br> Job: <a href=3D"http://www.ccl.net/jobs" rel=3D"noreferrer noreferrer" targ= et=3D"_blank">http://www.ccl.net/jobs</a> <br> Conferences: <a href=3D"http://server.ccl.net/chemistry/announcements/confe= rences/" rel=3D"noreferrer noreferrer" target=3D"_blank">http://server.ccl.= net/chemistry/announcements/conferences/</a><br> <br> Search Messages: <a href=3D"http://www.ccl.net/chemistry/searchccl/index.sh= tml" rel=3D"noreferrer noreferrer" target=3D"_blank">http://www.ccl.net/che= mistry/searchccl/index.shtml</a><br> <br<br> =C2=A0 =C2=A0 =C2=A0 <a href=3D"http://www.ccl.net/spammers.txt" rel=3D"nor= eferrer noreferrer" target=3D"_blank">http://www.ccl.net/spammers.txt</a><b= r> <br> RTFI: <a href=3D"http://www.ccl.net/chemistry/aboutccl/instructions/" rel= =3D"noreferrer noreferrer" target=3D"_blank">http://www.ccl.net/chemistry/a= boutccl/instructions/</a><br> <br> <br> </blockquote></div> --00000000000000319b0570a7c96f-- From owner-chemistry@ccl.net Tue Jul 10 14:52:00 2018 From: "Grzegorz Mazur mazur###chemia.uj.edu.pl" <owner-chemistry_-_server.ccl.net> To: CCL Subject: CCL: get electrostatic potential at atoms and molecular polarizability Message-Id: <-53387-180710144541-8462-9oT+U9FqEmbe9JzlUae78Q_-_server.ccl.net> X-Original-From: Grzegorz Mazur <mazur]|[chemia.uj.edu.pl> Content-Language: en-GB Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Tue, 10 Jul 2018 20:45:27 +0200 MIME-Version: 1.0 Sent to CCL by: Grzegorz Mazur [mazur:_:chemia.uj.edu.pl] Hi, Sorry, my first answer got mangled somehow. Two obvious suspects are Cartesian vs spherical basis set, as already suggested by David, and different variants of B3LYP (VWN3 vs VWN5 based). Grzesiek On 10.07.2018 14:38, Jorge Iulek iulek]~[uepg.br wrote: > > Sent to CCL by: Jorge Iulek [iulek(~)uepg.br] > Dear all, > > > I have some molecules structurally similar to ones that were used > in a previous (not by me) QSAR study. To these, a model (equation to > estimate biological activity) was proposed (very good correlation) to > explain (reasonably well) activities based on QM descriptors. Therefore > I want to check what the biological activity is estimated for my similar > molecules. I need to calculate the electrostatic potential (EP) at two > specific atoms and the molecule polarizability, to make the prediction. > I should say that the model was established using other QM program, > nevertheless, but I must go for the free academic program gamess. The > article states that the molecules were structure optimized (3D > gemometry) using DFT theory, the 6-31G(d) basis set at the hybrid > functional B3LYP. > > My gamess input for optimization contains: > ------------------------ > $contrl dfttyp=B3LYP runtyp=optimize nzvar=72 coord=zmt icharg=0 $end > $system timlim=525600.0 MWORDS=6 $end > $statpt hess=guess nstep=100 nprt=-1 npun=0 $end > $basis GBASIS=N31 NGAUSS=6 NDFUNC=1 $end > $guess guess=huckel $end > $SCF DIRSCF=.true. CONV=1d-7 FDIFF=.FALSE. $end > $DFT DFTTYP=B3LYP $end > ... here comes coordinates (as zmatrix), etc... > --------------------------- > > And then from the resulting .dat file I extract both $DATA and $VEC > lines to input with lines below to calculate EP... > ---------------- > $contrl runtyp=prop dfttyp=B3LYP nzvar=0 coord=unique icharg=0 $end > $system timlim=525600.0 MWORDS=6 $end > $basis GBASIS=N31 NGAUSS=6 NDFUNC=1 $end > $guess guess=moread $end > $DFT DFTTYP=B3LYP $end > $ELPOT IEPOT=1 WHERE=NUCLEI OUTPUT=BOTH $end > $FFCALC OFFDIA=.TRUE. $end > ... $DATA and $VEC ... > ------- > > And molecular polarizability with... > -------------- > $contrl runtyp=energy local=boys $end > $local poldcm=.true. polnum=.true. fcore=.false. $end > $contrl dfttyp=B3LYP nzvar=0 coord=unique icharg=0 $end > $SYSTEM MWORDS=6 $END > $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 $END > $GUESS GUESS=moread $END > $SCF DIRSCF=.true. CONV=1d-7 FDIFF=.FALSE. $end > $DFT DFTTYP=B3LYP $end > ... $DATA and $VEC ... > ------------ > > The matter is that with these instructions, even for the original > molecules (of the QSAR study), I cannot reproduce author's results. In > fact, the QSAR model (equation) seems to be quite sensitive to the > resulting EP (their coefficients in the equation are large, so minor > differences have large impact). Therefore, possibly I miss something > here at my input files for gamess. I would much thank if someone would > criticize my inputs and point to some error. Should I expect, in any > case, to get very approximate results, once the calculation implies the > same theory, basis set, functional, etc. (I guess), at using different > QM programs? > > Yours, > > > Jorge> > Conferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > From owner-chemistry@ccl.net Tue Jul 10 21:34:00 2018 From: "Alan Shusterman alan^_^reed.edu" <owner-chemistry]=[server.ccl.net> To: CCL Subject: CCL: get electrostatic potential at atoms and molecular polarizability Message-Id: <-53388-180710131141-5806-qnFGuHQYivgPpzzCA9hPVQ]=[server.ccl.net> X-Original-From: Alan Shusterman <alan_-_reed.edu> Content-Type: multipart/alternative; boundary="000000000000cae9d40570a838bc" Date: Tue, 10 Jul 2018 10:11:32 -0700 MIME-Version: 1.0 Sent to CCL by: Alan Shusterman [alan::reed.edu] --000000000000cae9d40570a838bc Content-Type: text/plain; charset="UTF-8" Jorge, You might pass along the article, or the procedure part of the article, that you are trying to reproduce. I'm not at all familiar with GAMESS input so I can't help you there, but if I had to guess at what your problem is I would say, look at *the location where the EP is calculated*. EP values change rapidly from extremely (and for most interpretive purposes, uselessly) positive near the atomic nucleus to zero at points far from the molecule. I will bet that you are interested in a location where the value is relatively modest (+/- 100-400 kJ/mol), but there can be considerable variation in these values too so it is necessary to follow the recipe used by the developers of the QSAR. Good luck, Alan On Tue, Jul 10, 2018 at 5:38 AM, Jorge Iulek iulek]~[uepg.br < owner-chemistry/./ccl.net> wrote: > > Sent to CCL by: Jorge Iulek [iulek(~)uepg.br] > Dear all, > > > I have some molecules structurally similar to ones that were used in a > previous (not by me) QSAR study. To these, a model (equation to estimate > biological activity) was proposed (very good correlation) to explain > (reasonably well) activities based on QM descriptors. Therefore I want to > check what the biological activity is estimated for my similar molecules. I > need to calculate the electrostatic potential (EP) at two specific atoms > and the molecule polarizability, to make the prediction. I should say that > the model was established using other QM program, nevertheless, but I must > go for the free academic program gamess. The article states that the > molecules were structure optimized (3D gemometry) using DFT theory, the > 6-31G(d) basis set at the hybrid functional B3LYP. > > My gamess input for optimization contains: > ------------------------ > $contrl dfttyp=B3LYP runtyp=optimize nzvar=72 coord=zmt icharg=0 $end > $system timlim=525600.0 MWORDS=6 $end > $statpt hess=guess nstep=100 nprt=-1 npun=0 $end > $basis GBASIS=N31 NGAUSS=6 NDFUNC=1 $end > $guess guess=huckel $end > $SCF DIRSCF=.true. CONV=1d-7 FDIFF=.FALSE. $end > $DFT DFTTYP=B3LYP $end > ... here comes coordinates (as zmatrix), etc... > --------------------------- > > And then from the resulting .dat file I extract both $DATA and $VEC > lines to input with lines below to calculate EP... > ---------------- > $contrl runtyp=prop dfttyp=B3LYP nzvar=0 coord=unique icharg=0 $end > $system timlim=525600.0 MWORDS=6 $end > $basis GBASIS=N31 NGAUSS=6 NDFUNC=1 $end > $guess guess=moread $end > $DFT DFTTYP=B3LYP $end > $ELPOT IEPOT=1 WHERE=NUCLEI OUTPUT=BOTH $end > $FFCALC OFFDIA=.TRUE. $end > ... $DATA and $VEC ... > ------- > > And molecular polarizability with... > -------------- > $contrl runtyp=energy local=boys $end > $local poldcm=.true. polnum=.true. fcore=.false. $end > $contrl dfttyp=B3LYP nzvar=0 coord=unique icharg=0 $end > $SYSTEM MWORDS=6 $END > $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 $END > $GUESS GUESS=moread $END > $SCF DIRSCF=.true. CONV=1d-7 FDIFF=.FALSE. $end > $DFT DFTTYP=B3LYP $end > ... $DATA and $VEC ... > ------------ > > The matter is that with these instructions, even for the original > molecules (of the QSAR study), I cannot reproduce author's results. In > fact, the QSAR model (equation) seems to be quite sensitive to the > resulting EP (their coefficients in the equation are large, so minor > differences have large impact). Therefore, possibly I miss something here > at my input files for gamess. I would much thank if someone would criticize > my inputs and point to some error. Should I expect, in any case, to get > very approximate results, once the calculation implies the same theory, > basis set, functional, etc. (I guess), at using different QM programs? > > Yours, > > > Jorgehttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: http://server.ccl.net/chemistr > y/announcements/conferences/> > > -- Alan Shusterman Chemistry Department Reed College 3203 SE Woodstock Blvd Portland, OR 97202-8199 503-517-7699 http://blogs.reed.edu/alan/ "Patience, persistence, and a sense of humor." Dave Barrett --000000000000cae9d40570a838bc Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable <div dir=3D"ltr"><div>Jorge,</div><div>You might pass along the article, or= the procedure part of the article, that you are trying to reproduce. I'= ;m not at all familiar with GAMESS input so I can't help you there, but= if I had to guess at what your problem is I would say, look at <u>the loca= tion where the EP is calculated</u>. EP values change rapidly from extremel= y (and for most interpretive purposes, uselessly) positive near the atomic = nucleus to zero at points far from the molecule. I will bet that you are in= terested in a location where the value is relatively modest (+/- 100-400 kJ= /mol), but there can be considerable variation in these values too so it is= necessary to follow the recipe used by the developers of the QSAR. Good lu= ck,</div><div>Alan<br></div></div><div class=3D"gmail_extra"><br><div class= =3D"gmail_quote">On Tue, Jul 10, 2018 at 5:38 AM, Jorge Iulek iulek]~[<a hr= ef=3D"http://uepg.br">uepg.br</a> <span dir=3D"ltr"><<a href=3D"mailto:o= wner-chemistry/./ccl.net" target=3D"_blank">owner-chemistry/./ccl.net</a>></= span> wrote:<br><blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8e= x;border-left:1px #ccc solid;padding-left:1ex"><br> Sent to CCL by: Jorge Iulek [iulek(~)<a href=3D"http://uepg.br" rel=3D"nore= ferrer" target=3D"_blank">uepg.br</a>]<br> Dear all,<br> <br> <br> =C2=A0=C2=A0=C2=A0 I have some molecules structurally similar to ones that = were used in a previous (not by me) QSAR study. To these, a model (equation= to estimate biological activity) was proposed (very good correlation) to e= xplain (reasonably well) activities based on QM descriptors. Therefore I wa= nt to check what the biological activity is estimated for my similar molecu= les. I need to calculate the electrostatic potential (EP) at two specific a= toms and the molecule polarizability, to make the prediction. I should say = that the model was established using other QM program, nevertheless, but I = must go for the free academic program gamess. The article states that the m= olecules were structure optimized (3D gemometry) using=C2=A0 DFT theory, th= e 6-31G(d) basis set at the hybrid functional B3LYP.<br> <br> =C2=A0=C2=A0=C2=A0 My gamess input for optimization contains:<br> ------------------------<br> =C2=A0$contrl dfttyp=3DB3LYP runtyp=3Doptimize nzvar=3D72 coord=3Dzmt ichar= g=3D0 $end<br> =C2=A0$system timlim=3D525600.0 MWORDS=3D6 $end<br> =C2=A0$statpt hess=3Dguess nstep=3D100 nprt=3D-1 npun=3D0 $end<br> =C2=A0$basis=C2=A0 GBASIS=3DN31 NGAUSS=3D6 NDFUNC=3D1 $end<br> =C2=A0$guess=C2=A0 guess=3Dhuckel $end<br> =C2=A0$SCF DIRSCF=3D.true. CONV=3D1d-7 FDIFF=3D.FALSE. $end<br> =C2=A0$DFT DFTTYP=3DB3LYP $end<br> ... here comes coordinates (as zmatrix), etc...<br> ---------------------------<br> <br> =C2=A0=C2=A0=C2=A0 And then from the resulting .dat file I extract both $DA= TA and $VEC lines to input with lines below to calculate EP...<br> ----------------<br> =C2=A0$contrl runtyp=3Dprop dfttyp=3DB3LYP nzvar=3D0 coord=3Dunique icharg= =3D0 $end<br> =C2=A0$system timlim=3D525600.0 MWORDS=3D6 $end<br> =C2=A0$basis=C2=A0 GBASIS=3DN31 NGAUSS=3D6 NDFUNC=3D1 $end<br> =C2=A0$guess guess=3Dmoread $end<br> =C2=A0$DFT DFTTYP=3DB3LYP $end<br> =C2=A0$ELPOT IEPOT=3D1 WHERE=3DNUCLEI OUTPUT=3DBOTH $end<br> =C2=A0$FFCALC OFFDIA=3D.TRUE. $end<br> ... $DATA and $VEC ...<br> -------<br> <br> =C2=A0=C2=A0=C2=A0 And molecular polarizability with...<br> --------------<br> =C2=A0$contrl runtyp=3Denergy local=3Dboys $end<br> =C2=A0$local=C2=A0 poldcm=3D.true. polnum=3D.true.=C2=A0 =C2=A0fcore=3D.fal= se.=C2=A0 $end<br> =C2=A0$contrl dfttyp=3DB3LYP nzvar=3D0 coord=3Dunique icharg=3D0 $end<br> =C2=A0$SYSTEM MWORDS=3D6 $END<br> =C2=A0$BASIS=C2=A0 GBASIS=3DN31 NGAUSS=3D6 NDFUNC=3D1 $END<br> =C2=A0$GUESS=C2=A0 GUESS=3Dmoread $END<br> =C2=A0$SCF DIRSCF=3D.true. CONV=3D1d-7 FDIFF=3D.FALSE. $end<br> =C2=A0$DFT DFTTYP=3DB3LYP $end<br> ... $DATA and $VEC ...<br> ------------<br> <br> =C2=A0=C2=A0=C2=A0 The matter is that with these instructions, even for the= original molecules (of the QSAR study), I cannot reproduce author's re= sults. In fact, the QSAR model (equation) seems to be quite sensitive to th= e resulting EP (their coefficients in the equation are large, so minor diff= erences have large impact). Therefore, possibly I miss something here at my= input files for gamess. I would much thank if someone would criticize my i= nputs and point to some error. Should I expect, in any case, to get very ap= proximate results, once the calculation implies the same theory, basis set,= functional, etc. (I guess), at using different QM programs?<br> <br> =C2=A0=C2=A0=C2=A0 Yours,<br> <br> <br> Jorge<br> <br> <br> <br> -=3D This is automatically added to each message by the mailing script =3D-= <br<br=<br<br> <br> E-mail to subscribers: <a href=3D"mailto:CHEMISTRY/./ccl.net" target=3D"_blan= k">CHEMISTRY/./ccl.net</a> or use:<br> =C2=A0 =C2=A0 =C2=A0<a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_mess= age" rel=3D"noreferrer" target=3D"_blank">http://www.ccl.net/cgi-bin/cc<wbr= >l/send_ccl_message</a><br> <br> E-mail to administrators: <a href=3D"mailto:CHEMISTRY-REQUEST/./ccl.net" targ= et=3D"_blank">CHEMISTRY-REQUEST/./ccl.net</a> or use<br> =C2=A0 =C2=A0 =C2=A0<a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_mess= age" rel=3D"noreferrer" target=3D"_blank">http://www.ccl.net/cgi-bin/cc<wbr= >l/send_ccl_message</a><br> <br> Subscribe/Unsubscribe:=C2=A0 =C2=A0 =C2=A0 <a href=3D"http://www.ccl.net/ch= emistry/sub_unsub.shtml" rel=3D"noreferrer" target=3D"_blank">http://www.cc= l.net/chemistry/s<wbr>ub_unsub.shtml</a><br> <br> Before posting, check wait time at: <a href=3D"http://www.ccl.net" rel=3D"n= oreferrer" target=3D"_blank">http://www.ccl.net</a><br> <br> Job: <a href=3D"http://www.ccl.net/jobs" rel=3D"noreferrer" target=3D"_blan= k">http://www.ccl.net/jobs</a> Conferences: <a href=3D"http://server.ccl.ne= t/chemistry/announcements/conferences/" rel=3D"noreferrer" target=3D"_blank= ">http://server.ccl.net/chemistr<wbr>y/announcements/conferences/</a><br> <br> Search Messages: <a href=3D"http://www.ccl.net/chemistry/searchccl/index.sh= tml" rel=3D"noreferrer" target=3D"_blank">http://www.ccl.net/chemistry/s<wb= r>earchccl/index.shtml</a><br> <br<br> =C2=A0 =C2=A0 =C2=A0<a href=3D"http://www.ccl.net/spammers.txt" rel=3D"nore= ferrer" target=3D"_blank">http://www.ccl.net/spammers.t<wbr>xt</a><br> <br> RTFI: <a href=3D"http://www.ccl.net/chemistry/aboutccl/instructions/" rel= =3D"noreferrer" target=3D"_blank">http://www.ccl.net/chemistry/a<wbr>boutcc= l/instructions/</a><br> <br> <br> </blockquote></div><br><br clear=3D"all"><br>-- <br><div class=3D"gmail_sig= nature" data-smartmail=3D"gmail_signature"><div dir=3D"ltr"><div><div dir= =3D"ltr">Alan Shusterman<br>Chemistry Department<br>Reed College<br>3203 SE= Woodstock Blvd<br>Portland, OR 97202-8199<br>503-517-7699<br><a href=3D"ht= tp://blogs.reed.edu/alan/" target=3D"_blank">http://blogs.reed.edu/alan/</a= ><br>"Patience, persistence, and a sense of humor." Dave Barrett<= br></div></div></div></div> </div> --000000000000cae9d40570a838bc--