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." Cheers, Oliver On Mon, Mar 12, 2012 at 12:42, dina dusti <[email protected]> wrote: > Thank you very much from your response. > > Best Regards > Dina > > ________________________________ > From: Justin A. Lemkul <[email protected]> > To: dina dusti <[email protected]>; Discussion list for GROMACS users > <[email protected]> > 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 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
