Hi Prasun, Indeed, there's more to the conversion of DNA for gromacs input. Some sed lines:
sed -e '{/^.\{13\}H.\'/d; /^.\{13\}H7. THY/d; /^.\{12\}H5''/d}' should get you rid of these hydrogens, and sed -e '{s/\(^.\{13\}C\)7 THY/\15M THY/}' should set the proper name for the DTHY methyl group. As I've mentioned, these lines come from a script I wrote. I just copy-pasted the sed portions, but I'm not sure that they work out of the box. I'll see if I can make the script independent of Haddock parameter files and make it available. It does use CNS though... Cheers, Tsjerk On Fri, Sep 19, 2008 at 3:26 PM, prasun kumar <[EMAIL PROTECTED]> wrote: > Hello Tsjerk > > I have solved that problem, now while running PDB2GMX command its giving > following error > > C7 was not found in rtp file > so I just compared the atom type in rtp file for DTHY and corresponding pdb > file and replace C7 by C5M. > i used -ignh option also,still I am getting warning like > H1 is not found > H3 is not found > > but the program is running its giving error while running GROMPP step. > can you please help me in removing this error > with regards > -- > PRASUN (ASHOKA) > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php