[gmx-users] CP atom type
Mark.Abraham at anu.edu.au
Fri Feb 10 06:03:48 CET 2006
Rongliang Wu wrote:
> Hello Mark,
> thanks for your suggestions, but the top file generated by the PRODRG server has charges for CH2 and CH3 groups, has the server made mistakes? is it that only united alcane carbon groups have zero charges?
I know nothing about PRODRG. ffgmx.rtp does actually have charges for
some of its CH2 & CH3 groups - I didn't look thoroughly last time.
Obviously, in general it would be reasonable for (united) atoms to have
partial charges where a chemist would expect redistribution of charge in
a molecule caused by the electronegativity of the constituent
atoms/groups. The converse also applies.
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