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
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling.stonybrook.edu
===================================================================
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 -----
>From: arubin.unmc.edu
>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
>>USA
>>E-mail: arubin.unmc.edu
>>WWW: http://www.unmc.edu/Eppley
>>
>>
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Received on Wed Feb 16 2005 - 13:53:00 PST
