[gmx-users] Re: How to use the dummy atom?

[Dallas Warren]

>   Can you tell me how to obatain the atomic charges. I think I can 
> calculate the atomic charge by a ab initio calculation. I don't know 
> which types of population analysis and atomic charge assignments will be 
> suitable. Can you give me some hints on how to get the atomic charges of 
> these molecules?

The simplest way is to go through the .rtp file for the forcefield that you 
are using and pick out similar charge groups in the molecules entered there 
that are similar to those within your molecule..  At least then the charges 
are most likely to have been set for the forcefield.  As someone a week or 
two ago on this list found out, the ab initio calculation produces larger 
charges than what is typically uses in charge groups for the force fields.

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy
Monash University
381 Royal Parade
Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9083
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