[gmx-users] Re: Thanks for your help!

Bruce D. Ray brucedray at yahoo.com
Tue Jan 31 15:18:25 CET 2012

I am replying to the Gromacs User's list rather than directly.

On Monday, January 30, 2012 12:38 AM,Tom <dnaafm at gmail.com>wrote:

> Thanks for answering me my question and thanks for the nice open 
> source code program!
> I found out my prvious problem due to the problem of my *mol2 file.

> Can you help with two more doubts?

> 1) Can you provide a reference for me if I want to cite your work of
> topolbuild program?

I have not published anything regarding topolbuild.  As noted in the source code
comments, when I wrote it, I borrowed heavily from other sources.

> 2) i am making a chemical structure, which contains 2 hydrocarbon (surgar ring) 
> connected with 2 H2PO4-. I tired to use topolbuild and oplsaa forcefield. I noticed
> oplss only has forcefield and partial charges MeOPO3H and MeOPO3--, but there 
> are no parameters available for H2PO4-. But the program of topolbuild works magically 
> to assign the charges, by whichthe overal is -2, which is exactly equal to the real
> situation (the total charges of my *mol2 file is -2) although the type of P is P???

Something has bothered me about the *.mol2 file excerpt you pasted in your original
e-mail.  It did not have correct Tripos atom types in the sixth column and totally lacked
the seventh, eighth, and ninth  columns that contain the atom segment number, the
residue name, and the atom charge which should be 0.0 for a molecule with NO_CHARGE
specified in the file heading.  I can only assume that what you pasted in your original
e-mail was not the file you actually used.

> I want to consult you what kind of algorithm that you used to assign the partial charges
> and make the total equal to the expected value?

The command you listed in your original e-mail would not assign charges, but would
take the charges given in the *.mol2 file.  For the excerpt of an *.mol2 that you pasted
in your original e-mail, these charges would be 0.0 because the heading read NO_CHARGE
If the -charge option is given in the command line, the charge for each atom type is
read from the parameters file for the selected force field found in the directory pointed
to by the -dir parameter.  The charges in the paramters files for these atom types and
force fields were copied from gromacs force field files.  This is not in any way a
sophisticated charge assignment.

> If you have time and want to look at my *mol file and the generated *top file, i can email
> to you. 

I had been under the impression that you had pasted an excerpt from your actual *.mol2
file although I do not see how that file could have been accepted as a valid *.mol2 file
by topolbuild


Bruce D. Ray, Ph.D.
Associate Scientist
Physics Dept.
402 N. Blackford St.
Indianapolis, IN  46202-3273
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