VMD-L Mailing List

From: Chris Harrison (charris5_at_gmail.com)
Date: Thu Apr 26 2012 - 06:23:08 CDT

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.
>
>
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-- 
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