[gmx-users] query about making a pdb file

Jay Mashl mashl at uiuc.edu
Thu Mar 29 21:07:50 CEST 2007

PyMOL (http://pymol.sf.net) is one option for building the chain based on 
natural amino acids and subsequently performing mutations.


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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