[gmx-users] pdb file

Oliver Stueker ostueker at gmail.com
Mon Mar 12 20:03:30 CET 2012

A neat way to get generic coordinates of organic molecules like this
is using Jmol:

1) go to http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm?USESIGNED
    This requires Sun/Oracle Java plugin activated in the browser and
asks for permission to trust the signed applet.
    Alternatively one could use the Jmol Application instead.

2) type the following two commands into the "cmd" textbox (or the Jmol console)
    load "$Thiophene" ;
    write coords "?" ;

The first one will load the structure and the second one will open a
Save-File dialog to ask for the filename to save it on your hard disk.

Quoting Bob Hanson (currently the lead Jmol developer): "If you can
name it [and if it is organic] [...] you can probably get it."


On Mon, Mar 12, 2012 at 12:42, dina dusti <dinadusti at yahoo.com> wrote:
> Thank you very much from your response.
> Best Regards
> Dina
> ________________________________
> From: Justin A. Lemkul <jalemkul at vt.edu>
> To: dina dusti <dinadusti at yahoo.com>; Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Sent: Monday, March 12, 2012 10:02 PM
> Subject: Re: [gmx-users] pdb file
> dina dusti wrote:
>> Dear Gromacs Specialists,
>> I need pdb file of tiofen, but I didn't find it!!!
>> Can I change pdb file of one compound that is as same as tiofen (for
>> example pyrrole) and give it to PRODRG for obtain gro file and topology file
>> of tiofen?
> There are numerous methods for producing coordinate files.  See, for
> instance:
> http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources
> -Justin

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