Its very unclear for me because after pdb2gmx -f 1.pdb -o conf.gro -ignh with gromos force field
I've checked conf.gro by VMD and this structure didnt contains any hydrogens ;o James 2011/10/31 Justin A. Lemkul <jalem...@vt.edu> > > > James Starlight wrote: > >> Dear Gromacs Users! >> >> I could not find how I can add missing hydrogens after their removing by >> pdb2gmx -ignh. >> >> I have modified structure of my protein after editing by some soft and I >> removed all hydrogens but now I want to add it back in accordance with >> gromos ff topology >> >> How I can do it ? >> >> > They are removed and rebuilt entirely by pdb2gmx in accordance with the > instructions found in the .hdb file. If there are no hydrogens in the > input, then -ignh is irrelevant. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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 gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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