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John,<br><br>
First off, search the archive for this list. The subject has come
up several times before.<br><br>
<blockquote type=cite class=cite cite>I am working on a non standard
ligand at the moment & <br>
wondered about defining partial charges on atoms. I have <br>
derived the partial charges using GAMESS with the 6-31G <br>
basis set. Can I just insert these into the .rtp file in <br>
the [ATOM] section for my ligand??? The other thing I was
</blockquote><br>
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.<br><br>
<blockquote type=cite class=cite cite>wondering was that GAMESS has
assigned partial charges to <br>
carbon atoms in one of the alyl chains in the ligand, but <br>
looking through the .rtp file only a small small percentage <br>
of the alkyl carbons in the existing force field have a <br>
charge assigned to them. Do I leave these charges out??
</blockquote><br>
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.<br><br>
Hope this helps.<br><br>
Catch ya,<br>
<x-sigsep><p></x-sigsep>
<b>Dr. Dallas Warren<br>
</b><i>Research Fellow<br>
</i>Department of Pharmaceutical Biology and Pharmacology<br>
Victorian College of Pharmacy, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
<font color="#0000FF"><u>dallas.warren@vcp.monash.edu.au<br>
</u></font>+61 3 9903 9083<br>
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