[gmx-users] query about making a pdb file

[Eric Jakobsson]

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 <jmondal at chem.wisc.edu>
>>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>To: Discussion list for GROMACS users <gmx-users at 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