From: DENILSON FERREIRA DE OLIVEIRA (denilson_at_dqi.ufla.br)
Date: Sun Apr 29 2012 - 18:58:39 CDT

Hi Chris.

Once more, thank you for being so kind.

Regarding the QMtoolplugin, I am using the version that you sent me by e-mail:

$Id: qmtool.tcl,v 1.47 2012/01/23 23:09:58 johns Exp $
$Id: qmtool_analysis.tcl,v 1.11 2009/06/22 16:45:08 saam Exp $
$Id: qmtool_atomedit.tcl,v 1.7 2005/11/24 18:04:11 saam Exp $
$Id: qmtool_aux.tcl,v 1.25 2012/02/23 15:02:46 gumbart Exp $
$Id: qmtool_charges.tcl,v 1.5 2012/01/07 21:30:39 gumbart Exp $
$Id: qmtool_intcoor.tcl,v 1.16 2007/09/12 13:41:59 saam Exp $
$Id: qmtool_readwrite.tcl,v 1.48 2012/02/23 15:02:47 gumbart Exp $
$Id: qmtool_setup.tcl,v 1.28 2007/03/02 12:14:12 saam Exp $

But I found in your page that there was a newer version of the qmtool_readwrite.tcl file:

$Id: qmtool_readwrite.tcl,v 1.50 2012/03/29 16:39:28 mayne Exp $

Then I replaced the old one with the version 1.50, but I could not solve the problem with the diferent angle definition between FFTK and Gaussian/GaussView.

I am using the windows version of VMD 1.9.1 (vmd191win32.msi) which I downloaded on February 6th 2012. Except for the 1.9.2 version (which is not stable yet) of this software, it seems to be the most up-to-date code.

Any suggestion/advice ?

Best regards.

Denilson.

Denilson F. Oliveira
Laboratório de Produtos Naturais
Departamento de Química
Universidade Federal de Lavras

----- Mensagem original -----
De: Christopher G Mayne <cmayne2_at_illinois.edu>
Para: vmd-l_at_ks.uiuc.edu
Cc: DENILSON FERREIRA DE OLIVEIRA <denilson_at_dqi.ufla.br>
Enviadas: Sun, 29 Apr 2012 18:28:16 -0300 (BRT)
Assunto: RE: vmd-l: Force Field ToolKit - Angles

Apparently FFTK/VMD 1.9.1 uses an angle definition that is a little bit different from Gaussian09/GaussView. In the first Gaussian input file below (a), generated by FFTK ("Water Int." window), there is no clash of the water molecule with my structure when I open this file in the VMD display. However, when I open this file with GaussView, the water molecule is clashing with one of the carboxylate groups. After the Gaussian calculation at the HF/6-31G* level of theory, the water molecule is clashing with the carboxylate group in both FFTK/VMD and GaussView. To circumvent this problem I had to multiply the H1w-C2-C1 angle by -1, resulting in the Gaussian input file below (b).

Some time ago we found a problem with how QMTool loads Gaussian files that utilize Z-matrix notation, where it wasn't using the proper sign for angles/dihedrals and led to this type of behavior. This bug was fixed some time ago. You may try checking that you are using the most up-to-date VMD code.

By the way, for alcohols and ethers FFTK generates only one structure where the oxygen of the alcohol (or ether) interacts with the hydrogen of water, and in this structure the angles C-O----H(from water) and H-O----H(from water) are around 120 degrees. In view of what I know (or I think to know) about hybridization of the oxygen atom these angles seem to be incorrect, but I suppose that it is necessary to keep the results consistent with the Charmm parameterization. OK ?

Remember that MM point charge models do not account for localization of electrons. See my recent response to your previous post regarding carbonyls. In this case, 120 degrees in the plane of the ether is the MM energy minimum. While ffTK will generate alternate water placements for carbonyls, it only generates the MM geometry for ethers.

Chris

Date: Sun, 29 Apr 2012 16:39:52 -0300 (BRT)
From: DENILSON FERREIRA DE OLIVEIRA <denilson_at_dqi.ufla.br<mailto:denilson_at_dqi.ufla.br>>
Subject: vmd-l: Force Field ToolKit - Angles

Dear Chris,

Apparently FFTK/VMD 1.9.1 uses an angle definition that is a little bit different from Gaussian09/GaussView. In the first Gaussian input file below (a), generated by FFTK ("Water Int." window), there is no clash of the water molecule with my structure when I open this file in the VMD display. However, when I open this file with GaussView, the water molecule is clashing with one of the carboxylate groups. After the Gaussian calculation at the HF/6-31G* level of theory, the water molecule is clashing with the carboxylate group in both FFTK/VMD and GaussView. To circumvent this problem I had to multiply the H1w-C2-C1 angle by -1, resulting in the Gaussian input file below (b).

By the way, for alcohols and ethers FFTK generates only one structure where the oxygen of the alcohol (or ether) interacts with the hydrogen of water, and in this structure the angles C-O----H(from water) and H-O----H(from water) are around 120 degrees. In view of what I know (or I think to know) about hybridization of the oxygen atom these angles seem to be incorrect, but I suppose that it is necessary to keep the results consistent with the Charmm parameterization. OK ?

Thank you again for your attention.

Best regards.

Denilson.

a) Gaussian input file generated by FFTK:

%chk=TSA-ACC-C2.chk
%nproc=3
%mem=100MB
# RHF/6-31G* Opt=(Z-matrix,MaxCycles=100)

<qmtool> simtype="Geometry optimization" </qmtool>
TSA-ACC-C2

- -2 1
C1 1.1979999542236328 -0.057999998331069946 -0.019999999552965164
C2 0.5899999737739563 0.17000000178813934 1.3329999446868896
C3 -0.47200000286102295 0.9760000109672546 1.534999966621399
C4 -1.1959999799728394 1.656000018119812 0.4230000078678131
O5 -1.1349999904632568 3.1059999465942383 0.6740000247955322
C6 -0.6029999852180481 1.340000033378601 -0.9629999995231628
C7 0.9020000100135803 1.1579999923706055 -0.8960000276565552
O8 -1.2319999933242798 0.21199999749660492 -1.590000033378601
C9 -0.9629999995231628 -1.090999960899353 -1.0099999904632568
C10 0.5299999713897705 -1.284000039100647 -0.6899999976158142
C11 2.740999937057495 -0.3440000116825104 0.07800000160932541
O12 3.140000104904175 -0.9419999718666077 1.1260000467300415
O13 3.431999921798706 0.014999999664723873 -0.9290000200271606
C14 -1.968999981880188 -1.531999945640564 0.11100000143051147
O15 -2.9660000801086426 -0.7860000133514404 0.3540000021457672
O16 -1.7079999446868896 -2.683000087738037 0.5849999785423279
H17 1.0399999618530273 -0.38100001215934753 2.1579999923706055
H18 -0.8939999938011169 1.0950000286102295 2.5350000858306885
H19 -2.24399995803833 1.3300000429153442 0.4230000078678131
H20 -1.8140000104904175 3.496000051498413 0.09200000017881393
H21 -0.8679999709129333 2.1760001182556152 -1.6299999952316284
H22 1.3170000314712524 1.003000020980835 -1.8969999551773071
H23 1.371000051498413 2.055999994277954 -0.46700000762939453
H24 -1.2050000429153442 -1.7710000276565552 -1.840999960899353
H25 0.6309999823570251 -2.1700000762939453 -0.05400000140070915
H26 1.0800000429153442 -1.4609999656677246 -1.6269999742507935
H1w C2 rAH C1 90.50 C3 90.91
 x H1w 1.0 C2 90.0 C1 0.0
Ow H1w 0.9572 x 90.0 C2 180.0
H2w Ow 0.9572 H1w 104.52 x dih

rAH 2.0
dih 0.0

b) Gaussian input file generated by FFTK and manually corrected (-1 x H1w-C2-C1):

%chk=TSA-ACC-C2.chk
%nproc=3
%mem=100MB
# RHF/6-31G* Opt=(Z-matrix,MaxCycles=100)

<qmtool> simtype="Geometry optimization" </qmtool>
TSA-ACC-C2

- -2 1
C1 1.1979999542236328 -0.057999998331069946 -0.019999999552965164
C2 0.5899999737739563 0.17000000178813934 1.3329999446868896
C3 -0.47200000286102295 0.9760000109672546 1.534999966621399
C4 -1.1959999799728394 1.656000018119812 0.4230000078678131
O5 -1.1349999904632568 3.1059999465942383 0.6740000247955322
C6 -0.6029999852180481 1.340000033378601 -0.9629999995231628
C7 0.9020000100135803 1.1579999923706055 -0.8960000276565552
O8 -1.2319999933242798 0.21199999749660492 -1.590000033378601
C9 -0.9629999995231628 -1.090999960899353 -1.0099999904632568
C10 0.5299999713897705 -1.284000039100647 -0.6899999976158142
C11 2.740999937057495 -0.3440000116825104 0.07800000160932541
O12 3.140000104904175 -0.9419999718666077 1.1260000467300415
O13 3.431999921798706 0.014999999664723873 -0.9290000200271606
C14 -1.968999981880188 -1.531999945640564 0.11100000143051147
O15 -2.9660000801086426 -0.7860000133514404 0.3540000021457672
O16 -1.7079999446868896 -2.683000087738037 0.5849999785423279
H17 1.0399999618530273 -0.38100001215934753 2.1579999923706055
H18 -0.8939999938011169 1.0950000286102295 2.5350000858306885
H19 -2.24399995803833 1.3300000429153442 0.4230000078678131
H20 -1.8140000104904175 3.496000051498413 0.09200000017881393
H21 -0.8679999709129333 2.1760001182556152 -1.6299999952316284
H22 1.3170000314712524 1.003000020980835 -1.8969999551773071
H23 1.371000051498413 2.055999994277954 -0.46700000762939453
H24 -1.2050000429153442 -1.7710000276565552 -1.840999960899353
H25 0.6309999823570251 -2.1700000762939453 -0.05400000140070915
H26 1.0800000429153442 -1.4609999656677246 -1.6269999742507935
H1w C2 rAH C1 -90.50 C3 90.91
 x H1w 1.0 C2 90.0 C1 0.0
Ow H1w 0.9572 x 90.0 C2 180.0
H2w Ow 0.9572 H1w 104.52 x dih

rAH 2.0
dih 0.0

Prof. Dr. Denilson F. OliveiraLaboratÓrio de Produtos NaturaisDepartamento de QuÖmicaUniversidade Federal de LavrasCaixa Postal 3037Lavras - MG - BrasilCEP 37.200-000Tel: (55)(35) 3829-1623Fax: (55)(35) 3829-1271e-mail: denilson_at_dqi.ufla.br<mailto:denilson_at_dqi.ufla.br>

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