Re: [gmx-users] doubts on g_confrms output
Hi, The error message says the number of atoms in the first frame is not what was expected. That indicates the reference structure didn't match, which suggests the pdb file with the fitted structures wasn't used as reference. Solution: give the fitted structures both as reference (-s) and as trajectory (-f) with trjconv. Cheers, Tsjerk On Feb 12, 2011 2:19 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 12/02/2011 3:45 AM, Kwee Hong wrote: Hi Mark, I tried but with this error: Fatal erro... OK. I don't know why two frames with different numbers of atoms are written. Maybe g_confrms -one is useful. Or you can chop apart the PDB by hand in a text editor. Mark From: Mark Abraham mark.abra...@anu.edu.au To: Discussion... -- 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] doubts on g_confrms output
On 12/02/2011 7:07 PM, Tsjerk Wassenaar wrote: Hi, The error message says the number of atoms in the first frame is not what was expected. That indicates the reference structure didn't match, which suggests the pdb file with the fitted structures wasn't used as reference. Solution: give the fitted structures both as reference (-s) and as trajectory (-f) with trjconv. From the contents of the .pdb file the OP posted, I think the different number of atoms in each PDB model is a feature/bug of g_confrms. The documentation doesn't make clear what the output should be, however. Mark Cheers, Tsjerk On Feb 12, 2011 2:19 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 12/02/2011 3:45 AM, Kwee Hong wrote: Hi Mark, I tried but with this error: Fatal erro... OK. I don't know why two frames with different numbers of atoms are written. Maybe g_confrms -one is useful. Or you can chop apart the PDB by hand in a text editor. Mark From: Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au To: Discussion... -- 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 -- 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] doubts on g_confrms output
On 2011-02-12 02.19, Mark Abraham wrote: On 12/02/2011 3:45 AM, Kwee Hong wrote: Hi Mark, I tried but with this error: Fatal error: Number of atoms in pdb frame 0 is 331 instead of 491 OK. I don't know why two frames with different numbers of atoms are written. Maybe g_confrms -one is useful. Or you can chop apart the PDB by hand in a text editor. Mark *From:* Mark Abraham mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Saturday, February 12, 2011 0:01:39 *Subject:* Re: [gmx-users] doubts on g_confrms output On 12/02/2011 2:55 AM, Kwee Hong wrote: Hi Tsjerk, Thanks for the help. I got it. But do you have any idea how to solve this in vmd? Use trjconv -sep on the .pdb file to split it. Mark Regards, Joyce *From:* Tsjerk Wassenaar tsje...@gmail.com *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Saturday, January 22, 2011 15:53:22 *Subject:* Re: [gmx-users] doubts on g_confrms output Hi Joyce, In pymol use 'set all_states' Cheers, Tsjerk On Jan 22, 2011 8:30 AM, Kwee Hong jestan1...@yahoo.com mailto:jestan1...@yahoo.com wrote: Hi, I was trying to do some analysis following John's GROMACS tutorial for solvation study of spider toxin peptide. I'm using GROMACS-4.5.3 and my command line for g_confrms is g_confrms -f1 1OMB.pdb -f2 md.gro -o fit_wet.pdb If e.g. 1OMB.pdb does not have hydrogen and md.gro does, you need to specify two index files, pointint to e.g. the C-alpha atoms. Then the fit can be done on these and your superposition will be fine. The program calculated the RMSD sucessfully and fit_wet.pdb was generated. Yet, when i tried to visualise fit_wet.pdb using VMD, the structure is obviously in a mess. And when I tried it out with pymol, I can only visualised one model. Model 2 did not appear. I wonder would it be the pdb format generated by g_confrms is not the standard pdb format and had caused VMD and final failed to read them? Herein, I attached part of the pdb file generated by fit_wet.pdb. Any insight is welcomed. Thanks, Joyce -- 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 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] doubts on g_confrms output
Hoi :)
Maybe the following lines are useful. First, to extract the first
model from a PDB file:
sed /ENDMDL/q trajectory.pdb first.pdb
Just for the record, to extract a specific frame # from a PDB file:
sed -ne '{/^MODEL *# /,/ENDMDL/p}' trajectory.pdb frame-#.pdb (NOTE:
replace # with the number)
Then, to extract the last frame from a PDB file:
sed -ne '/^MODEL/,/^ENDMDL/{/^MODEL/{x;d};H}' -e '${x;p}'
trajectory.pdb last.pdb
With these lines it does not matter whether the frames/models have
equal (numbers of) atoms or not.
Hope it helps,
Tsjerk
On Sat, Feb 12, 2011 at 10:09 AM, David van der Spoel
sp...@xray.bmc.uu.se wrote:
On 2011-02-12 02.19, Mark Abraham wrote:
On 12/02/2011 3:45 AM, Kwee Hong wrote:
Hi Mark,
I tried but with this error:
Fatal error:
Number of atoms in pdb frame 0 is 331 instead of 491
OK. I don't know why two frames with different numbers of atoms are
written. Maybe g_confrms -one is useful. Or you can chop apart the PDB
by hand in a text editor.
Mark
*From:* Mark Abraham mark.abra...@anu.edu.au
*To:* Discussion list for GROMACS users gmx-users@gromacs.org
*Sent:* Saturday, February 12, 2011 0:01:39
*Subject:* Re: [gmx-users] doubts on g_confrms output
On 12/02/2011 2:55 AM, Kwee Hong wrote:
Hi Tsjerk,
Thanks for the help. I got it.
But do you have any idea how to solve this in vmd?
Use trjconv -sep on the .pdb file to split it.
Mark
Regards,
Joyce
*From:* Tsjerk Wassenaar tsje...@gmail.com
*To:* Discussion list for GROMACS users gmx-users@gromacs.org
*Sent:* Saturday, January 22, 2011 15:53:22
*Subject:* Re: [gmx-users] doubts on g_confrms output
Hi Joyce,
In pymol use 'set all_states'
Cheers,
Tsjerk
On Jan 22, 2011 8:30 AM, Kwee Hong jestan1...@yahoo.com
mailto:jestan1...@yahoo.com wrote:
Hi,
I was trying to do some analysis following John's GROMACS tutorial
for solvation study of spider toxin peptide.
I'm using GROMACS-4.5.3 and my command line for g_confrms is
g_confrms -f1 1OMB.pdb -f2 md.gro -o fit_wet.pdb
If e.g. 1OMB.pdb does not have hydrogen and md.gro does, you need to specify
two index files, pointint to e.g. the C-alpha atoms. Then the fit can be
done on these and your superposition will be fine.
The program calculated the RMSD sucessfully and fit_wet.pdb was
generated. Yet, when i tried to visualise fit_wet.pdb using VMD, the
structure is obviously in a mess. And when I tried it out with
pymol, I can only visualised one model. Model 2 did not appear. I
wonder would it be the pdb format generated by g_confrms is not the
standard pdb format and had caused VMD and final failed to read them?
Herein, I attached part of the pdb file generated by fit_wet.pdb.
Any insight is welcomed.
Thanks,
Joyce
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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
--
gmx-users mailing list gmx-users@gromacs.org
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--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] doubts on g_confrms output
Hi Tsjerk, Thanks for the help. I got it. But do you have any idea how to solve this in vmd? Regards, Joyce From: Tsjerk Wassenaar tsje...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, January 22, 2011 15:53:22 Subject: Re: [gmx-users] doubts on g_confrms output Hi Joyce, In pymol use 'set all_states' Cheers, Tsjerk On Jan 22, 2011 8:30 AM, Kwee Hong jestan1...@yahoo.com wrote: Hi, I was trying to do some analysis following John's GROMACS tutorial for solvation study of spider toxin peptide. I'm using GROMACS-4.5.3 and my command line for g_confrms is g_confrms -f1 1OMB.pdb -f2 md.gro -o fit_wet.pdb The program calculated the RMSD sucessfully and fit_wet.pdb was generated. Yet, when i tried to visualise fit_wet.pdb using VMD, the structure is obviously in a mess. And when I tried it out with pymol, I can only visualised one model. Model 2 did not appear. I wonder would it be the pdb format generated by g_confrms is not the standard pdb format and had caused VMD and final failed to read them? Herein, I attached part of the pdb file generated by fit_wet.pdb. Any insight is welcomed. Thanks, Joyce -- 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] doubts on g_confrms output
On 12/02/2011 2:55 AM, Kwee Hong wrote: Hi Tsjerk, Thanks for the help. I got it. But do you have any idea how to solve this in vmd? Use trjconv -sep on the .pdb file to split it. Mark Regards, Joyce *From:* Tsjerk Wassenaar tsje...@gmail.com *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Saturday, January 22, 2011 15:53:22 *Subject:* Re: [gmx-users] doubts on g_confrms output Hi Joyce, In pymol use 'set all_states' Cheers, Tsjerk On Jan 22, 2011 8:30 AM, Kwee Hong jestan1...@yahoo.com mailto:jestan1...@yahoo.com wrote: Hi, I was trying to do some analysis following John's GROMACS tutorial for solvation study of spider toxin peptide. I'm using GROMACS-4.5.3 and my command line for g_confrms is g_confrms -f1 1OMB.pdb -f2 md.gro -o fit_wet.pdb The program calculated the RMSD sucessfully and fit_wet.pdb was generated. Yet, when i tried to visualise fit_wet.pdb using VMD, the structure is obviously in a mess. And when I tried it out with pymol, I can only visualised one model. Model 2 did not appear. I wonder would it be the pdb format generated by g_confrms is not the standard pdb format and had caused VMD and final failed to read them? Herein, I attached part of the pdb file generated by fit_wet.pdb. Any insight is welcomed. Thanks, Joyce -- 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 -- 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] doubts on g_confrms output
Hi Mark, I tried but with this error: Fatal error: Number of atoms in pdb frame 0 is 331 instead of 491 Joyce From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, February 12, 2011 0:01:39 Subject: Re: [gmx-users] doubts on g_confrms output On 12/02/2011 2:55 AM, Kwee Hong wrote: Hi Tsjerk, Thanks for the help. I got it. But do you have any idea how to solve this in vmd? Use trjconv -sep on the .pdb file to split it. Mark Regards, Joyce From: Tsjerk Wassenaar tsje...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, January 22, 2011 15:53:22 Subject: Re: [gmx-users] doubts on g_confrms output Hi Joyce, In pymol use 'set all_states' Cheers, Tsjerk On Jan 22, 2011 8:30 AM, Kwee Hong jestan1...@yahoo.com wrote: Hi, I was trying to do some analysis following John's GROMACS tutorial for solvation study of spider toxin peptide. I'm using GROMACS-4.5.3 and my command line for g_confrms is g_confrms -f1 1OMB.pdb -f2 md.gro -o fit_wet.pdb The program calculated the RMSD sucessfully and fit_wet.pdb was generated. Yet, when i tried to visualise fit_wet.pdb using VMD, the structure is obviously in a mess. And when I tried it out with pymol, I can only visualised one model. Model 2 did not appear. I wonder would it be the pdb format generated by g_confrms is not the standard pdb format and had caused VMD and final failed to read them? Herein, I attached part of the pdb file generated by fit_wet.pdb. Any insight is welcomed. Thanks, Joyce -- 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] doubts on g_confrms output
On 12/02/2011 3:45 AM, Kwee Hong wrote: Hi Mark, I tried but with this error: Fatal error: Number of atoms in pdb frame 0 is 331 instead of 491 OK. I don't know why two frames with different numbers of atoms are written. Maybe g_confrms -one is useful. Or you can chop apart the PDB by hand in a text editor. Mark *From:* Mark Abraham mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Saturday, February 12, 2011 0:01:39 *Subject:* Re: [gmx-users] doubts on g_confrms output On 12/02/2011 2:55 AM, Kwee Hong wrote: Hi Tsjerk, Thanks for the help. I got it. But do you have any idea how to solve this in vmd? Use trjconv -sep on the .pdb file to split it. Mark Regards, Joyce *From:* Tsjerk Wassenaar tsje...@gmail.com *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Saturday, January 22, 2011 15:53:22 *Subject:* Re: [gmx-users] doubts on g_confrms output Hi Joyce, In pymol use 'set all_states' Cheers, Tsjerk On Jan 22, 2011 8:30 AM, Kwee Hong jestan1...@yahoo.com mailto:jestan1...@yahoo.com wrote: Hi, I was trying to do some analysis following John's GROMACS tutorial for solvation study of spider toxin peptide. I'm using GROMACS-4.5.3 and my command line for g_confrms is g_confrms -f1 1OMB.pdb -f2 md.gro -o fit_wet.pdb The program calculated the RMSD sucessfully and fit_wet.pdb was generated. Yet, when i tried to visualise fit_wet.pdb using VMD, the structure is obviously in a mess. And when I tried it out with pymol, I can only visualised one model. Model 2 did not appear. I wonder would it be the pdb format generated by g_confrms is not the standard pdb format and had caused VMD and final failed to read them? Herein, I attached part of the pdb file generated by fit_wet.pdb. Any insight is welcomed. Thanks, Joyce -- 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 -- 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] doubts on g_confrms output
Hi Joyce, In pymol use 'set all_states' Cheers, Tsjerk On Jan 22, 2011 8:30 AM, Kwee Hong jestan1...@yahoo.com wrote: Hi, I was trying to do some analysis following John's GROMACS tutorial for solvation study of spider toxin peptide. I'm using GROMACS-4.5.3 and my command line for g_confrms is g_confrms -f1 1OMB.pdb -f2 md.gro -o fit_wet.pdb The program calculated the RMSD sucessfully and fit_wet.pdb was generated. Yet, when i tried to visualise fit_wet.pdb using VMD, the structure is obviously in a mess. And when I tried it out with pymol, I can only visualised one model. Model 2 did not appear. I wonder would it be the pdb format generated by g_confrms is not the standard pdb format and had caused VMD and final failed to read them? Herein, I attached part of the pdb file generated by fit_wet.pdb. Any insight is welcomed. Thanks, Joyce -- 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
