[gmx-users] query about making a pdb file
mashl at uiuc.edu
Fri Mar 30 00:23:31 CEST 2007
See 'help save'. Apparently there is no menu option for saving the 'all' group.
On Thu, 29 Mar 2007, Jagannath Mondal wrote:
> Date: Thu, 29 Mar 2007 16:41:35 -0500
> From: Jagannath Mondal <jmondal at chem.wisc.edu>
> To: Jay Mashl <mashl at uiuc.edu>,
> Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] query about making a pdb file
> Thanks, But is it possible to get the corresponding PDB format of that
> molcule from pymol after drawing it? Basically, I installed the pymol. But
> I could not find an option for writing the corresponding PDB structure of
> the entire molecule
> On Mar 29, 2007, at 2:07 PM, Jay Mashl wrote:
>> 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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