[gmx-users] query about making a pdb file

[Jagannath Mondal]

Hi,
    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
   Jagannath

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.
>
> 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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