Look, in order to use editconf and gen box one need first to have gro and top files, which are generated by pdb2gmx. You say I don't need it. Ok may be topology file can be written by hand, but what about "gro" file?
--- On Mon, 5/31/10, Mark Abraham <mark.abra...@anu.edu.au> wrote: > From: Mark Abraham <mark.abra...@anu.edu.au> > Subject: Re: [gmx-users] water clusters MD > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Date: Monday, May 31, 2010, 10:55 AM > ----- Original Message ----- > From: Oleksandr <nablaobl...@yahoo.com> > Date: Monday, May 31, 2010 18:48 > Subject: [gmx-users] water clusters MD > To: gmx-users@gromacs.org > > > Hi, > > I'm new user of Gromacs. There are plenty examples how > to do > > solvation study of various proteins. But I'd like to > "solvate" > > highly ordered heavy water clusters in box of light > water. At > > the first step when I execute "pdb2gmx -f > watercluster.pdb" I > > get an error no matter which model is chosen: > > > ------------------------------------------------------- > > > > Fatal error: > > Atom H in residue HOH 4 not found in rtp entry with 3 > atoms > > while sorting atoms. Maybe > different protonation state. > > Remove this hydrogen or choose a > different > > protonation state. > > Option -ignh will ignore all > hydrogens in the input. > > > ------------------------------------------------------- > > > > Can anybody help me how to solve this problem? > > You're using a tool for a different job. pdb2gmx builds a > topology file, mostly by constructing a [moleculetype] from > a polymer of repeating units. Your moleculetypes are > trivial, and at least one is already present in an .itp file > for use with #include. > > editconf and genbox make a box and fill it with generic > solvent. It will be simplest to either write your .top by > hand, or adapt an existing .top, depending what you mean by > "heavy water". Either way, you'll need some fluency with > GROMACS workflows and file types, so do all the general > tutorial material you can find. If you'd done so, you might > have realised that pdb2gmx is not really the tool for the > job. > > Mark > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
