Another handy bit of software for model building is Ecce
http://ecce.emsl.pnl.gov/
At 02:07 PM 3/29/2007, you wrote:
PyMOL (http://pymol.sf.net) is one option for building the chain
based on natural amino acids and subsequently performing mutations.
Jay
On Wed, 28 Mar 2007, Jagannath Mondal wrote:
Date: Wed, 28 Mar 2007 23:54:27 -0500
From: Jagannath Mondal <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Subject: [gmx-users] query about making a pdb file
Hi all,
I am a gromacs beginner. I am dealing with a 10-residue molecule
each of which is un-natural amino acid called beta-peptide. I was
wondering whether there is any option of making a PDB file so that
I can use it to prepare the corresponding .gro file in gromacs. I
somehow could generate the cartesian coordinates of the
molecule. At least, can you suggest some software which are free
and have mac-version so that I can generate the coresponding PDB
file of the molecule from the cartesian coordinates.
Thanks,
Jagannath Mondal
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---------------------------------
Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of
Biochemistry, and of the Center for Biophysics and Computational Biology
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
3261 Beckman Institute, mc251
University of Illinois, Urbana, IL 61801
ph. 217-244-2896 Fax 217 244 9757
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