----- Original Message ----- From: Oleksandr <nablaobl...@yahoo.com> Date: Tuesday, June 1, 2010 11:39 Subject: Re: [gmx-users] water clusters MD To: Discussion list for GROMACS users <gmx-users@gromacs.org>
> 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 You need neither file for editconf and genbox. See http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#On_the_need_for_a_.gro_file. You can use your existing correctly-formatted .pdb file. If you already have a .top for the original structure, genbox will update it suitably with the new waters. Mark > 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 -- 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