AMBER Archive (2007)

Subject: Re: AMBER: using amber for cyclic peptides

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Mon Oct 15 2007 - 12:53:54 CDT

Quoting rebeca_at_mmb.pcb.ub.es:

> I am quite new in AMBER, and I am interested in carrying a molecular dynamics
> calculation of a system containing an aminocyclohexanecarboxyl and
> aminocypentanecarboxyl acid. I have found a paper tittled “Improved Treatment
> of Cyclic B-Amino Acids and Successful Prediction of B-Peptide Secondary
> Structure Using a Modified Force Field: AMBER*C” (Journal of Computational
> Chemistry, Vol. 21, No. 9, 763–773 (2000), where they added parameters to the
> AMBER force field to model cyclic B-amino acid derivatives more accurately
> within the commonly used MacroModel program.
> Does anyone know about this implementation in the AMBER program? Can
> you tell me
> which force field, if there is any, implemented in Amber 9.0 can I
> use to treat
> these type of cyclic peptides? Should I add extra parameters?

You could use those parameters or derive your own set of force field
libraries starting from capped amino-acid analogs. See the tutorial of
R.E.D.-III
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php
and in particular
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#10

Then, see how to use Tripos mol2 files as force field libraries in LEaP
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#15

And see a new tutorial written by C. Cezard @
   -I.3.3.5- Using Tripos mol2 files in LEaP: Implementation of new
features in LEaP
http://q4md-forcefieldtools.org/Tutorial/leap.php

regards, Francois

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