exactly all hydrogens were represented as a part of the groupd in wich they were. So is there possible way to explicit it?
Another question about pdb2gmx. about -term as I understood this must be used only if atoms for CAP groups are presented in the PDB file mustnt it? So what term exactly do? Doest it make a connection beetween CAP and C and N termi or anothing else? James 2011/10/31 Justin A. Lemkul <[email protected]> > > > James Starlight wrote: > >> 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 >> >> > I highly doubt that. I've used one of the Gromos96 force fields for > nearly all of my work and it has never failed in any Gromacs version. > Perhaps you're simply not taking into account the fact that Gromos96 > parameter sets are united atom, meaning that aliphatic hydrogens are not > represented explicitly. > > > -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 [email protected] > 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 [email protected]. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
-- 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
