Re: AMBER: Cyclic peptide

From: Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) <>
Date: Wed, 16 Feb 2005 10:48:19 +0100

It depends on the cyclicization tipe and on the format of the starting
structure. If you have a PDB format starting structure Leap can read
it, but can not understand if you want a ciclic peptide or not. If you
make the peptide cyclic with a disulphide bond, you have to chenge the
residue name of your CYS to CYX and then use the BOND command in leap
to make the bond between the sulphur atoms (after having removed the
hydrogens) . If you have a head to tail cyclic peptide you have to
connect the proper atoms (N and C) by the same command. Leap adds by
default zwitterionic C and N terminal aminioacids. You have to edit
your structure by removing the extra atoms you don't need (it is
possible to do it via grafical interface) , and then edit the atom
properties of the atoms of the former terminal residues, if necessary
(and probably it will be, check the total charge by the CHECK command
or by 'calculate net charge' in the grafical interface). You can find
the correct values for the central residues atom charges (that may be
different form terminal residues ones) in the prep files (all_amino94
or whatever you are using).
It may happen (it depend on the starting geometry you supply) that the
new bond drawn by leap is rather long. In such cases it's obviously
better to carefully minimize before starting the dynamic.

Stefano Pieraccini

----- Original Message -----
Date: Tuesday, February 15, 2005 10:12 pm
Subject: AMBER: Cyclic peptide

> Dear AMBER-users,
> I would like to carry out MD simulations for cyclic 25-residue
> peptide by
> ABMER 7. We have built reasonable initial coordinates for of this
> peptide
> by SYBYL (TRIPOS Inc.). How can I build the cyclic peptide and
> close the
> termini by the LEaP means?
> I would very appreciate if you can help.
> Thank you very much for you consideration.
> Alexander Rubinstein, Ph.D.
> UNMC Eppley Cancer Center
> Molecular Modeling Core Facility
> _________________________________
> University of Nebraska Medical Center
> 986805 Nebraska Medical Center
> Omaha, Nebraska 68198-6805
> E-mail:
> WWW:
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Received on Wed Feb 16 2005 - 09:53:00 PST
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