From: Bennion, Brian (Bennion1_at_llnl.gov)
Date: Thu Apr 26 2012 - 13:27:45 CDT

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