VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Apr 26 2012 - 12:41:38 CDT

On Thu, Apr 26, 2012 at 12:37 PM, <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

this is not "a lot". this is "nothing".
please keep in mind that VMD uses
single precision floating point numbers
internally and not all fractions can be
perfectly well represented in floating point.
you can easily tell from the individual
charges, since Tcl intermittently converts
all floating point numbers to double
precision before printing them.
single precision floating point has only
7 digits accuracy to begin with and if
you sum up numbers of varying magnitude
that drops to less.

axel.

> 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 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.