AMBER Archive (2008)

Subject: AMBER: ligand partial charge and conformation question

From: Dong Xu (d1xu_at_ucsd.edu)
Date: Thu Jun 26 2008 - 13:01:31 CDT

Hi,

I understand that ligand partial charges (either resp or am1-bcc) are
obtained after geometry optimization from a given initial ligand
conformation, say, from crystal structure. My confusion here is that since
partial charges depend on ligand conformation, would that be incorrect if I
load the initial ligand conformation and the partial charges calculated from
the optimized conformation for the preparation of prmtop/inpcrd files?

Thanks,

-DX

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