1. pdb2gmx, editconf and then solvate. 2. use trjconv and make a pdb. 3. Take 7 water molecules and put them in the top of your original pdb and start again from there.
On 3 June 2010 09:34, NG HUI WEN <huiwen...@nottingham.edu.my> wrote: > Looks like I’ve got some work to do. Thanks Mark! > > > > *From:* gmx-users-boun...@gromacs.org [mailto: > gmx-users-boun...@gromacs.org] *On Behalf Of *Mark Abraham > *Sent:* Thursday, June 03, 2010 4:27 PM > *To:* Discussion list for GROMACS users > *Subject:* Re: [gmx-users] pdb2gmx renumbers the residues in my pdb file > > > > > > ----- Original Message ----- > From: NG HUI WEN <huiwen...@nottingham.edu.my> > Date: Thursday, June 3, 2010 18:08 > Subject: [gmx-users] pdb2gmx renumbers the residues in my pdb file > To: gmx-users@gromacs.org > > > Hi, > > > > > > I’m a new gromacs user. I have encountered a problem with pdb2gmx where > it automatically renumbers the residues in my pdb file. > > > > > > For instance, the first residue in my protein F8 has become F1 – this > affects all the residues in the protein, something I find rather > inconvenient. > > > > > > I’ve been searching the archive for previous posts which might have a > solution to this but no luck so far. I might have been wrong. Many thanks > for your help. > > > I think you're out of luck. IIRC the facility you want is implemented in > the development version, but not yet released. If you re-renumber by hand, > then I suspect everything will be fine after that. grompp just needs > something whose atom and residue naming and ordering matches the .top... how > you produce that doesn't matter to it. > > Mark << > > Email has been scanned for viruses by UNMC email management > service<http://www.nottingham.edu.my> > > >> > << > > Email has been scanned for viruses by UNMC email management > service<http://www.nottingham.edu.my> > >> > > -- > 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 >
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