Thank you, Francois. I have found the messages from Carlos Simmerling.
My understanding from those messages is that the charge difference is negligable compared to the assumptions of molecular mechanics and there are no terms in the AMBER forcefield enforcing chirality such as improper torsions in CNS. When I read a pdb file using standard residue names, but with inverted chirality and leap assigns atom types, charges and paramaters without complaint, so I hope this correct.
regards,
Krisztina
--- On Tue, 6/18/13, FyD wrote:
> From: FyD
> Subject: Re: [AMBER] D amino acids
> To: "amber"
> Date: Tuesday, June 18, 2013, 4:33 PM
> 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
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
>
http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 18 2013 - 08:30:11 PDT
