[gmx-users] small molecule partial charges

Dallas Warren dallas.warren at vcp.monash.edu.au
Thu Jun 19 00:06:01 CEST 2003


First off, search the archive for this list.  The subject has come up 
several times before.

>I am working on a non standard ligand at the moment &
>wondered about defining partial charges on atoms. I have
>derived the partial charges using GAMESS with the 6-31G
>basis set. Can I just insert these into the .rtp file in
>the [ATOM] section for my ligand??? The other thing I was

 From what has been said previously, no you don't do this.  The partial 
charges from quantum calculations are significantly (x2?) more than what is 
typically implemented in the values used for a MD simulation.  To be the 
most consistent with the force field that you are using, probably the best 
bet is to pick out groups from other residues that have already been 
defined for that force field, and then use those partial charges.

>wondering was that GAMESS has assigned partial charges to
>carbon atoms in one of the alyl chains in the ligand, but
>looking through the .rtp file only a small small percentage
>of the alkyl carbons in the existing force field have a
>charge assigned to them. Do I leave these charges out??

Also, from what I can tell here is the residues are simplified and charges 
are only distributed around local groups i.e. 3-4 atoms.  Neighbouring 
groups are then handled on their own i.e. charges are kept local.

Hope this helps.

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
When the only tool you own is a hammer, every problem begins to resemble a nail.
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