AMBER Archive (2009)
Subject: [AMBER] Force field parameter for Unionized Phenylalanine HOOC-CH(NH2)-CH2-C6H5
From: Madhurima Jana (tinni.217_at_gmail.com)
Date: Fri Jun 19 2009 - 01:40:43 CDT
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.
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