VMD-L Mailing List

From: Bennion, Brian (Bennion1_at_llnl.gov)
Date: Fri Apr 27 2012 - 11:57:18 CDT

Hello,

This is helpful for when the psf file has already been correctly created.
It is unclear if the resulting psf file from psfgen routine has created the psf file with the correct charges.
That is why I asked for the reader to post his final psf file, note just what the charges vmd outputs to the command line. Vmd may be confused, but the psf file might still be ok.

Maybe I missed the initial post that had the final psf file attached.

Brian

-----Original Message-----
From: Ahmet Bakan [mailto:lordnapi_at_gmail.com]
Sent: Friday, April 27, 2012 9:27 AM
To: Bennion, Brian
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: Problem with generating psf using CGENFF

Hi Folks,

A resolution for this issue is available in VMD 1.9.1. When you add NAMD flag to the PSF file that contains long atom names and types, charges and other data are parsed correctly. This is the very first line in PSF file that might read "PSF CMAP". Append NAMD to make it read "PSF CMAP NAMD". This fixed my issued when using CGenFF.

Ahmet

On Fri, Apr 27, 2012 at 10:23 AM, Bennion, Brian <Bennion1_at_llnl.gov> wrote:

        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