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 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 listgmx-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 listgmx-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
Re: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching.
Natalie Stephenson 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. Are you making manual updates, or allowing genbox/genion to make changes for you? In the case of the former, check your work :) In the case of the latter, I'd be more concerned. There really is nothing diagnostic that can be done. You simply have to check how many of each molecule are in your system. Something has gone wrong somewhere along the way. http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology -Justin Can anyone throw some light on what I've gone wrong!! Thanks loads! Natalie -- 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 listgmx-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
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.ukmailto: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 listgmx-users@gromacs.orgmailto: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.orgmailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-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
RE: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching.
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. 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.ukmailto: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 listgmx-users@gromacs.orgmailto: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.orgmailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-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
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 listgmx-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 listgmx-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
RE: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching.
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 listgmx-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 listgmx-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 listgmx-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
