AMBER Archive (2004)

Subject: Re: AMBER: how to neutralize the peptide

From: Chris Moth (Chris.Moth_at_vanderbilt.edu)
Date: Wed Oct 27 2004 - 11:57:23 CDT

At 09:10 PM 10/26/2004, Ye Mei wrote:
>Dear Amber users£¬
>
>Could anyone tell me how to neutrolize the peptide in leap.

See section 3.5.2 of the Amber 7 or 8 manual for handling the
terminals. You can use protecting groups, or protonation/deprotonaiton, by
altering your input .PDB.

As for side chains, the table lists residue names for protonated ASP and
GLU residues. If you need a neutral ARG (?!?) it appears will have to
fabricate that residue yourself.

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