Re: Add acetyle and amin Group to peptide

From: Axel Kohlmeyer (
Date: Mon Dec 30 2013 - 03:55:11 CST

Terminal groups are applied through patches. Please see the psfgen docs and tutorials for details.
Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.

-----Original Message-----
From: Alireza Mansouri <>
Sender: owner-namd-l_at_ks.uiuc.eduDate: Mon, 30 Dec 2013 01:30:19
Reply-To: Alireza Mansouri <>
Subject: namd-l: Add acetyle and amin Group to peptide

I am going to add Acetyle and Amin group
for N-terminal and C-terminal to peptide. But the problem is that
after preparation of pdb file (preparation by Hyperchem OR Gabedit) during construction to psf the added
groups autonomously are removed by command segment U {pdb         .....pdb} .

Any one can help me in this problem?


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