Re: [AMBER] Fwd: azobenzene atoms name in amber format

From: David A Case <>
Date: Fri, 11 Sep 2020 11:24:26 -0400

On Fri, Sep 11, 2020, Aashish Bhatt wrote:

>*antechamber -i mk-pop.log -fi gout -o aza-prim.mol2 -fo mol2 -c resp -rn
>AZA -pf y -at amber*
>I have a query can I take the force field parameter for the whole unit in
>gaff2 instead of ff14SB.

You can, but peptides are generally better described with Amber force
fields that have been extensively optimized for that sort of molecule.

>the size of my system is 5 amino acid long wherein N-terminal azobenzene is
>connected and C-terminal NH2(NHE) was attached.

Please note that antechamber is designed to be used for single residues,
not for entire polypeptide chains. The basic approach to generating
force field parameters for modified amino acids is outlined here:

although this may be a bit out of date, the ideas should get you going.

[Developers and students: we could really use an up-to-date tutorial
here...maybe just updating this one, hopefully adding a second example,
and getting this onto the standard Amber tutorials webpage, rather than
"hidden" in the antechamber folder as above.]


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Received on Fri Sep 11 2020 - 08:30:02 PDT
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