Hi all,
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.
Any suggestion will highly be accepted.
Thanks,
Madhurima
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 06 2009 - 10:06:09 PDT
