AMBER Archive (2007)

Subject: AMBER: using amber for cyclic peptides

From: rebeca_at_mmb.pcb.ub.es
Date: Mon Oct 15 2007 - 12:23:50 CDT

Hello,
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?

Thanks a lot in advance for your help,

Rebeca García Fandiño Ph.D.
Parc Cientific de Barcelona
08028 Barcelona
e-mail: rebeca_at_mmb.pcb.ub.es

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