Dear Madhurima,
> Can anyone please inform me how to get the prmtop file for Unionized
> Phenylalanine (NH2-phe-COOH) which has terminal groups NH2 and COOH. I
> want to use this unionized form in MD simulation. In Amber forcefield
> for proteins all the parameters are given for ionized phenylalanine
> (NPHE, CPHE) and another having residue name PHE which contains only
> NH and C=O as terminal groups. So how shall I get Unionized
> Phenylalanine having structure HOOC-CH(NH2)-CH2-C6H5.
Yes, such a molecule is not available in the Amber FF topology database.
This is a "whole" molecule, i.e. not a fragment: Did you try to derive
RESP charges as for any type of other whole molecule ?
You first need to select the right conformation(s), and then run the
charge derivation.
The FF atom types will be the same than these in the central fragment
except for the terminal groups NH2 and COOH which present sp3 amine,
sp2 carbonyl and hydroxyl.
regards, Francois
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Received on Mon Jul 06 2009 - 10:06:42 PDT
