Dear Krisztina,
> Do I have to derive a separate topology file, .lib file, for D amino acids?
Two enantiomers have the same charge values (if the
'exact/corresponding' orientations are involved in MEP computation).
> Charges and atom types I imagine would be same.
Yes, although putting a D-amino-acid in the middle of L-amino-acids
leads to diastereoisomers, which would have different charge values
and identical atom types.
If I remember Simmerling's group has published a work about charge
values and diastereoisomers. I am sure people in this list know this
reference...
> It is not clear to me if there is an improper term that is applied
> to the inverted chirality.
Simply transform the x coordinates into -x.
regards, Francois
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Received on Tue Jun 18 2013 - 08:00:03 PDT
