From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Apr 30 2012 - 15:26:07 CDT

On Apr 30, 2012, at 3:22 PM, DENILSON FERREIRA DE OLIVEIRA wrote:

>
> Finally, I would like to ask again about the scaling factor of 0.89 that should be applied to the MP2/6-31G* force constant matrix. May be some of you (or somebody else) could tell me if this scaling us used in the calculations carried out in the "Calc. Bonded" window of FFTK.
>

I believe it is, but you could always just grep the code for 0.89 to confirm.

JC

> Thank you very much for your attention
>
> Best regards.
>
> Denilson.
>
>
> Prof. Dr. Denilson F. OliveiraLaboratório de Produtos NaturaisDepartamento de QuímicaUniversidade Federal de LavrasCaixa Postal 3037Lavras - MG - BrasilCEP 37.200-000Tel: (55)(35) 3829-1623Fax: (55)(35) 3829-1271e-mail: denilson_at_dqi.ufla.br
>
> ----- Mensagem original -----
> De: Wang Yi <dexterwy_at_gmail.com>
> Para: DENILSON FERREIRA DE OLIVEIRA <denilson_at_dqi.ufla.br>
> Cc: vmd-l_at_ks.uiuc.edu, cmayne2_at_illinois.edu, gumbart_at_ks.uiuc.edu
> Enviadas: Sun, 29 Apr 2012 21:56:10 -0300 (BRT)
> Assunto: Re: vmd-l: Force Field ToolKit - Angles
>
> Hi Denilson,
>
> Which step are you at in the FFTK? The hydrogen bond optimization? Can't you get away by using Cartesian coordinates for water molecules?
>
> When I was playing with FFTK (terrific tool!) about two months ago, I remember that I didn't need Z-matrix format until the Hessian matrix step (angle/dihedral optimization).
>
> Best,
>
>
> ___________________________
>
> Yi (Yves) Wang
> Duke University
>
>
>
>
>
> On 2012-4-29, at 下午7:58, DENILSON FERREIRA DE OLIVEIRA wrote:
>
>> 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 But I found in your page that there was a newer version of the qmtool_readwrite.tcl file: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>
>>
>> ------------------------------
>>
>>
>
>