From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sun Apr 29 2012 - 14:57:33 CDT

Which version of ffTK are you using? I corrected a problem with the dihedral angle a couple months ago (post 1.9.1 release) that may be the root cause of what you observe. (For that matter, a lot of changes have been made, so you might find it worthwhile to get the latest alpha build anyway).

Chris is probably better able to comment on the second question.

-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of DENILSON FERREIRA DE OLIVEIRA
Sent: Sunday, April 29, 2012 2:40 PM
To: vmd-l_at_ks.uiuc.edu
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 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