----- Original Message ----- From: Oleksandr <nablaobl...@yahoo.com> Date: Tuesday, June 1, 2010 12:43 Subject: Re: [gmx-users] water clusters MD To: Discussion list for GROMACS users <gmx-users@gromacs.org>
> It would be helpful if you could be more specific. For example, > the standard procedure described in tutorial: > > pdb2gmx -f input.pdb > edit conf -f conf.gro d 0.5 -o newbox.gro > genbox -cp newbox.gro -cs spc2165.gro -p topol.top -o solvated.pdb > > Now, could you please illustrate how would you do this for > "trivial" non-protein molecules? editconf -d 0.5 -f pentamer.pdb -o newbox.gro genbox -cp newbox.gro -cs -o solvated.gro You can get some more information with editconf -h and genbox -h. Mark > --- On Tue, 6/1/10, 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: Tuesday, June 1, 2010, 4:16 AM > > ----- 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- > us...@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 > > > > > > > -- > 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
