VMD-L Mailing List

From: Chris Harrison (charris5_at_gmail.com)
Date: Thu Apr 26 2012 - 11:55:08 CDT

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