Yeah ... hadn't realised they were there when I began the simulating Natalie xxx ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: 22 September 2010 13:37 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching.
Natalie Stephenson wrote: > Ok ... think I've worked out what's happened ... > There were two 'SOL' groups. So when replacing solvent with ions it has > added double the amount of ions to the topol.top file. Think I'll go > back a couple of steps and try to sort out why there are two 'SOL' groups. Were there water molecules (i.e., from a crystal structure) in the initial structure passed to pdb2gmx? -Justin > Thanks for the help! > xxx > > > ------------------------------------------------------------------------ > *From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on > behalf of Natalie Stephenson [natalie.stephen...@postgrad.manchester.ac.uk] > *Sent:* 22 September 2010 13:02 > *To:* Discussion list for GROMACS users > *Subject:* RE: [gmx-users] Energy minimisation problems - coordinate > file and topology file not matching. > > Thanks for your help Justin & Terry > > I've been letting genion etc update it ... so there must be somewhere > where i've missed it or something. I'll check through the files and see > if I can see what's missing... > > xxx > > ------------------------------------------------------------------------ > *From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on > behalf of Terry [terrence...@gmail.com] > *Sent:* 22 September 2010 11:55 > *To:* Discussion list for GROMACS users > *Subject:* Re: [gmx-users] Energy minimisation problems - coordinate > file and topology file not matching. > > > Hi, Natalie, > > Obviously, number of coordinates still doesn't match the topology file > even you updated the topol.top *carefully*. > Check the topol.top thoroughly or paste several line of your coordinate > and topology files may be good ideas. > > Note that the topology file is lacking information for *28* atoms. Does > that number remind you anything? > > > Terry > > On Wed, Sep 22, 2010 at 6:42 PM, Natalie Stephenson > <natalie.stephen...@postgrad.manchester.ac.uk > <mailto:natalie.stephen...@postgrad.manchester.ac.uk>> wrote: > > Hi everyone, > > I was hoping you could clear up a problem I'm having when performing > energy minimisation. I'm following the instructions from one of the > tutorials (Justin's Umbrella Sampling) with my own protein, however, > this time when I try to perform the energy minimisation it throws > out this 'fatal error message' ... > > number of coordinates in coordinate file (nrr_solv_ions.gro, 33181) > does not match topology (topol.top, 33153) > > I've been updating the topol.top file every time I've done > something, so I'm not really sure what's happened. > > Can anyone throw some light on what I've gone wrong!! > Thanks loads! > Natalie > > -- > gmx-users mailing list gmx-users@gromacs.org > <mailto:gmx-users@gromacs.org> > 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 gmx-users-requ...@gromacs.org > <mailto:gmx-users-requ...@gromacs.org>. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- ======================================== 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 ======================================== -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
