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From: Bennion, Brian (Bennion1_at_llnl.gov)
Date: Fri Apr 27 2012 - 09:23:34 CDT
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Hello,
The topology or psf file would be more useful to see. In any case, it should be straight forward (read tedious) just to rename the atom type in the topology/parameter files to something shorter. It might be that the columns are shifted when psfgen reads in the topology due to the long atom type descriptions.
Brian
________________________________________
From: amin_at_imtech.res.in [amin_at_imtech.res.in]
Sent: Thursday, April 26, 2012 9:34 PM
To: Bennion, Brian
Cc: vmd-l_at_ks.uiuc.edu
Subject: RE: vmd-l: Problem with generating psf using CGENFF
There are some long atom types in the parameters generated by CGENFF as CG2R66,
NG2R50 etc. Can this be the problem? Is there a way out?
Here is the pdb file:
ATOM 1 F1 IGN 1 -6.687 -11.110 0.110 1.00 0.00 I F
ATOM 2 C1 IGN 1 -7.605 -7.719 0.976 1.00 0.00 I C
ATOM 3 H1 IGN 1 -7.344 -6.701 0.707 1.00 0.00 I H
ATOM 4 N1 IGN 1 -9.907 -9.467 3.335 1.00 0.00 I N
ATOM 5 S1 IGN 1 -9.290 -12.000 4.381 1.00 0.00 I S
ATOM 6 O1 IGN 1 -11.987 -12.824 5.198 1.00 0.00 I O
ATOM 7 C10 IGN 1 -12.420 -15.132 6.877 1.00 0.00 I C
ATOM 8 H10 IGN 1 -13.229 -14.673 4.571 1.00 0.00 I H
ATOM 9 C11 IGN 1 -12.192 -16.058 5.700 1.00 0.00 I C
ATOM 10 H11 IGN 1 -12.734 -18.235 3.719 1.00 0.00 I H
ATOM 11 C12 IGN 1 -12.619 -16.112 3.212 1.00 0.00 I C
ATOM 12 H12 IGN 1 -12.534 -19.016 1.422 1.00 0.00 I H
ATOM 13 C13 IGN 1 -12.636 -17.491 2.939 1.00 0.00 I C
ATOM 14 H13 IGN 1 -12.278 -14.973 0.013 1.00 0.00 I H
ATOM 15 C14 IGN 1 -12.524 -17.951 1.629 1.00 0.00 I C
ATOM 16 H14 IGN 1 -12.475 -14.142 2.319 1.00 0.00 I H
ATOM 17 C15 IGN 1 -12.395 -17.041 0.589 1.00 0.00 I C
ATOM 18 C16 IGN 1 -12.380 -15.675 0.834 1.00 0.00 I C
ATOM 19 C17 IGN 1 -12.493 -15.214 2.143 1.00 0.00 I C
ATOM 20 C2 IGN 1 -8.566 -7.952 1.957 1.00 0.00 I C
ATOM 21 H2 IGN 1 -9.031 -7.088 2.421 1.00 0.00 I H
ATOM 22 N2 IGN 1 -11.081 -10.094 5.088 1.00 0.00 I N
ATOM 23 O2 IGN 1 -11.547 -17.089 5.842 1.00 0.00 I O
ATOM 24 F2 IGN 1 -12.283 -17.488 -0.672 1.00 0.00 I F
ATOM 25 H3 IGN 1 -8.441 -11.373 1.941 1.00 0.00 I H
ATOM 26 C3 IGN 1 -8.925 -9.268 2.313 1.00 0.00 I C
ATOM 27 N3 IGN 1 -11.557 -8.917 4.592 1.00 0.00 I N
ATOM 28 C4 IGN 1 -8.272 -10.338 1.677 1.00 0.00 I C
ATOM 29 H4 IGN 1 -6.224 -8.603 -0.418 1.00 0.00 I H
ATOM 30 N4 IGN 1 -10.885 -8.554 3.511 1.00 0.00 I N
ATOM 31 C5 IGN 1 -7.312 -10.081 0.704 1.00 0.00 I C
ATOM 32 H5 IGN 1 -9.008 -13.218 6.469 1.00 0.00 I H
ATOM 33 N5 IGN 1 -11.281 -14.233 6.898 1.00 0.00 I N
ATOM 34 C6 IGN 1 -6.976 -8.784 0.343 1.00 0.00 I C
ATOM 35 H6 IGN 1 -9.826 -11.674 6.713 1.00 0.00 I H
ATOM 36 N6 IGN 1 -12.721 -15.551 4.516 1.00 0.00 I N
ATOM 37 C7 IGN 1 -10.098 -10.449 4.294 1.00 0.00 I C
ATOM 38 H7 IGN 1 -10.537 -14.431 7.562 1.00 0.00 I H
ATOM 39 C8 IGN 1 -9.767 -12.546 6.055 1.00 0.00 I C
ATOM 40 H8 IGN 1 -12.427 -15.713 7.804 1.00 0.00 I H
ATOM 41 C9 IGN 1 -11.134 -13.190 5.997 1.00 0.00 I C
ATOM 42 H9 IGN 1 -13.355 -14.567 6.798 1.00 0.00 I H
END
Thanks and Regards.
Amin.
> How many characters are the atom types in the pdb file?
> Psfgen has issues with really large atom types that come from cgenff.
> Brian
>
> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
> amin_at_imtech.res.in
> Sent: Thursday, April 26, 2012 10:27 AM
> To: Chris Harrison
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: Problem with generating psf using CGENFF
>
> Thanks again.I think I didn't explain correctly. I meant that if I add the
> partial charges as written in the str file (saved as rtf) obtained from
> paramchem, I get almost zero charge.But when I supply these same parameters to
> vmd, the generated psf file contains a non intergral large charge. You can
> please check it yourself using the files I attached. I am not using mol2 file
> for generating the psf/pdb pair, i am just using a pdb file of my ligand. For
> psf/pdb pair generation I am only using vmd 1.9.1, not any server. I really
> appreciate your help.
>
> Warm regards.
>
> Amin.
>
>
>
>
>> Amin,
>>
>> You'll need to check that the CGENFF topologies you're using between VMD and
> the server are the same. If they are, you should not be getting differing
> charge values.
>>
>> If you are using a mol2 for input to vmd to generate the psf/pdb pair, you may
> want to insure that you aren't including charges in the mol2 file that being
> propagated, as the charges should be defined by the topology.
>>
>> Best,
>> Chris
>>
>>
>> On Thu, Apr 26, 2012 at 11:37 AM, <amin_at_imtech.res.in> wrote:
>>> Thanks Chris. But that's what the problem is. This is the psf made by vmd
> from
>>> the parameters obtained from CGENFF. Below you can see that the mol2 file
> that
>>> I
>>> uploaded to CGENFF had negligible charge and also if I add up the partial
> charges generated by the server I get almost no charge but when vmd makes the
> psf file, suddenly a whole lot of charge appers.
>>> (VMD) 1 % set sel [atomselect top all]
>>> atomselect0
>>>>Main< (VMD) 2 % $sel get charge
>>> -0.12890000641345978 -0.092000000178813934 0.15199999511241913
>>> 0.011500000022351742 -0.098399996757507324 -0.62010002136230469
> 0.019999999552965164 0.34450000524520874 0.63910001516342163
>>> 0.17700000107288361
>>> 0.053599998354911804 0.15000000596046448 -0.13500000536441803
>>> 0.14800000190734863 -0.14000000059604645 0.14000000059604645
>>> 0.093900002539157867 -0.14000000059604645 -0.15700000524520874
>>> -0.12399999797344208 0.1679999977350235 -0.42199999094009399
>>> -0.58910000324249268 -0.1429000049829483 0.16899999976158142
>>> 0.032800000160932541 -0.02199999988079071 -0.18400000035762787
>>> 0.15999999642372131 -0.17579999566078186 0.14790000021457672
>>> 0.12870000302791595
>>> -0.55190002918243408 -0.15800000727176666 0.11370000243186951
>>> -0.46309998631477356 0.43979999423027039 0.34650000929832458
>>> -0.13930000364780426 0.096699997782707214 0.66710001230239868
>>> 0.085699997842311859
>>>>Main< (VMD) 3 % $sel get name
>>> F1 C1 H1 N1 S1 O1 C10 H10 C11 H11 C12 H12 C13 H13 C14 H14 C15 C16 C17 C2 H2
> N2
>>> O2 F2 H3 C3 N3 C4 H4 N4 C5 H5 N5 C6 H6 N6 C7 H7 C8 H8 C9 H9
>>>>Main< (VMD) 4 % get_total_charge
>>> 0.0019999807700514793
>>> From rtf file prepared using CGENFF:
>>> Charge
>>> -0.202
>>> -0.171
>>> 0.115
>>> 0.178
>>> -0.162
>>> -0.51
>>> -0.017
>>> 0.319
>>> 0.501
>>> 0.115
>>> 0.145
>>> 0.194
>>> -0.18
>>> 0.194
>>> -0.089
>>> 0.115
>>> 0.116
>>> -0.089
>>> -0.18
>>> -0.099
>>> 0.115
>>> -0.634
>>> -0.524
>>> -0.202
>>> 0.187
>>> 0.071
>>> -0.024
>>> -0.136
>>> 0.194
>>> -0.357
>>> 0.129
>>> 0.09
>>> -0.452
>>> -0.095
>>> 0.09
>>> -0.473
>>> 0.739
>>> 0.312
>>> -0.053
>>> 0.09
>>> 0.55
>>> 0.09
>>> Sum=-3.05311E-16
>>> Any help would be highly appreciated.
>>> Thanks.
>>> Amin.
>>>> You need to examine your partial charges. See below:
>>>> Best,
>>>> Chris
>>>>>Main< (dld) 4 % set sel [atomselect top all]
>>>> atomselect1
>>>>>Main< (dld) 5 % $sel get charge
>>>> -0.20200000703334808 1.0 0.11500000208616257 1.0 -0.16200000047683716
> -0.5099999904632568 -0.017000000923871994 0.3190000057220459
>>>> 0.5009999871253967 0.11500000208616257 1.0 0.1940000057220459 1.0
> 0.1940000057220459 1.0 0.11500000208616257 6.0 1.0 1.0 1.0
>>>> 0.11500000208616257 0.0 -0.5239999890327454 -0.20200000703334808
> 0.18700000643730164 1.0 0.0 1.0 0.1940000057220459 0.0 6.0
>>>> 0.09000000357627869 -0.4519999921321869 1.0 0.09000000357627869
> -0.4729999899864197 3.0 0.31200000643730164 -0.05299999937415123
> 0.09000000357627869 0.550000011920929 0.09000000357627869
>>>>>Main< (dld) 6 % $sel get name
>>>> F1 C1 H1 N1 S1 O1 C10 H10 C11 H11 C12 H12 C13 H13 C14 H14 C15 C16 C17 C2 H2
> N2 O2 F2 H3 C3 N3 C4 H4 N4 C5 H5 N5 C6 H6 N6 C7 H7 C8 H8 C9 H9
>>>>>Main< (dld) 7 % get_total_charge
>>>> 26.676000081002712
>>>>>Main< (dld) 8 %
>>>> On Thu, Apr 26, 2012 at 4:42 AM, <amin_at_imtech.res.in> wrote:
>>>>> Dear all,
>>>>> I am trying to generate the psf file for a small molecule using
>>>>> parameters
>>>>> generated by CGENFF but I am getting very high non integral charges. I am
> using the command "vmd -dispdev text -e ign.pgn". I have attached the
> required files. Can someone please help me with this?
>>>>> Warm Regards.
>>>>> Amin.
>>>>> ______________________________________________________________________
> सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
> Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
> सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036
>>>>> दूरभाष/EPABX :0172 6665 201-202
>>>> --
>>>> Chris Harrison, Ph.D.
>>>> NIH Center for Macromolecular Modeling and Bioinformatics
>>>> Theoretical and Computational Biophysics Group
>>>> Beckman Institute for Advanced Science and Technology
>>>> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>>>> http://www.ks.uiuc.edu/Research/namd Voice: 773-570-6078
> http://www.ks.uiuc.edu/~char Fax: 217-244-6078
>>> ______________________________________________________________________
> सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) Institute
> of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सैक्टर 39 ए,
> चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036
>>> दूरभाष/EPABX :0172 6665 201-202
>>
>>
>>
>> --
>> Chris Harrison, Ph.D.
>> NIH Center for Macromolecular Modeling and Bioinformatics
>> Theoretical and Computational Biophysics Group
>> Beckman Institute for Advanced Science and Technology
>> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>>
>> http://www.ks.uiuc.edu/Research/namd Voice: 773-570-6078
> http://www.ks.uiuc.edu/~char Fax: 217-244-6078
>>
>
>
>
>
> ______________________________________________________________________
> सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
> Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
> सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
> पिन कोड/PIN CODE :160036
> दूरभाष/EPABX :0172 6665 201-202
>
>
______________________________________________________________________
सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
पिन कोड/PIN CODE :160036
दूरभाष/EPABX :0172 6665 201-202
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