AMBER Archive (2009)

Subject: Re: [AMBER] adding a standard amino acid as ligand

• Previous message: S.Sundar Raman: "[AMBER] Issue related to vector saving"
• In reply to: sheerychen: "[AMBER] adding a standard amino acid as ligand"
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Dear sheerychen,

> Hello, everyone. I want to add a standard amino acid (lysine) as the ligand
> to the protein complex. Is there any method to deal with this ligand just
> with xleap or I have to deal with it as normal ligand with antechamber? I
> add TER before and after it, but leap will just treat it as normal
> C-terminal acid.

Amber FFs do not contain any 'isolated' amino-acid in their topology
database. This means you will have to generate the force field library
for this amino-acid; in its zwitterion or neutral form ?

Or you can use the dipeptide version of the amino-acid (AA) i.e. ACE-AA-NME...

regards, Francois

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• Previous message: S.Sundar Raman: "[AMBER] Issue related to vector saving"
• In reply to: sheerychen: "[AMBER] adding a standard amino acid as ligand"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]