Re: AMBER: Cyclic peptide

From: Carlos Simmerling <>
Date: Wed, 16 Feb 2005 08:00:29 -0500

yes, it looks like it is name mapping. tleap is converting your
N and C terminal residues to charged versions.
use "clearpdbresmap" to stop that, it is discussed more on page
48 of the amber8 manual. then it looks everything else is ok.

Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web:
Stony Brook, NY 11794-5115 E-mail:

Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) wrote:

>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
>>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
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Received on Wed Feb 16 2005 - 13:53:00 PST
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