Re: [gmx-users] top2psf.pl is generating some bonds to atoms with index 0.
Alright.. I actually simulated my protein for 5ns. Then I loaded the trajectory file and .gro file in vmd. Then, I extracted one of the frame and write it into pdb format, When I open it with vmd, one of the atom from a residue is connected to another atom in another residue. Things like this happens as VMD uses a distance-based bond determination heuristic. Therefore, I would need a structure file which specifies the bonds for my structure so that VMD doesn't have to guess. So how can I generate the structure file I needed? Thanks. Regards, Joyce From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Wednesday, October 20, 2010 2:25:26 Subject: Re: [gmx-users] top2psf.pl is generating some bonds to atoms with index 0. Kwee Hong wrote: I executed the script at the therminal by typing perl top2psf.pl -i topol.top -o zz.psf Here, I attached my input file. Your topology does not correspond to a MARTINI coarse-grained topology. As such, probably a bunch of the pattern matching is getting incorrect information. You cannot use top2psf.pl with this type of topology. It was created for a very specific purpose and requires that format, nothing else. -Justin *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Wednesday, October 20, 2010 2:14:34 *Subject:* Re: [gmx-users] top2psf.pl is generating some bonds to atoms with index 0. Kwee Hong wrote: Hi, I've got a top2psf.pl script from the web and used it to generate a psf file. Yet it generated some bonds to atoms with index 0 which should not occur. It causes VMD cannot load it and had a segmentation fault. vmd Info) Using plugin psf for structure file /home/birg/Desktop/zz.psf ERROR) Error reading bond information. Segmentation fault I wonder am I getting the right top2psf.pl. Or is there any place I can get the latest stable version of that script? There is only one version. Zeros are only printed if something goes wrong, i.e. you have provided the wrong input or something else has failed. Based solely on the information you've provided I cannot diagnose what has gone wrong. -Justin Here, I attached the perl script I used. Thanks. Regards, Joyce -- 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 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
Re: [gmx-users] top2psf.pl is generating some bonds to atoms with index 0.
Kwee Hong wrote: Alright.. I actually simulated my protein for 5ns. Then I loaded the trajectory file and .gro file in vmd. Then, I extracted one of the frame and write it into pdb format, When I open it with vmd, one of the atom from a residue is connected to another atom in another residue. Things like this happens as VMD uses a distance-based bond determination heuristic. Therefore, I would need a structure file which specifies the bonds for my structure so that VMD doesn't have to guess. So how can I generate the structure file I needed? I've never tried it myself, but editconf purports to write CONECT records when it extracts a structure from a .tpr file. You could construct a .tpr using the desired frame, then try to convert it to a .pdb file with CONECT records. Other than that, there may be some VMD tricks to get it to work, but I can't comment there. -Justin Thanks. Regards, Joyce *From:* Justin A. Lemkul jalem...@vt.edu *To:* Gromacs Users' List gmx-users@gromacs.org *Sent:* Wednesday, October 20, 2010 2:25:26 *Subject:* Re: [gmx-users] top2psf.pl is generating some bonds to atoms with index 0. Kwee Hong wrote: I executed the script at the therminal by typing perl top2psf.pl -i topol.top -o zz.psf Here, I attached my input file. Your topology does not correspond to a MARTINI coarse-grained topology. As such, probably a bunch of the pattern matching is getting incorrect information. You cannot use top2psf.pl with this type of topology. It was created for a very specific purpose and requires that format, nothing else. -Justin *From:* Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Sent:* Wednesday, October 20, 2010 2:14:34 *Subject:* Re: [gmx-users] top2psf.pl is generating some bonds to atoms with index 0. Kwee Hong wrote: Hi, I've got a top2psf.pl script from the web and used it to generate a psf file. Yet it generated some bonds to atoms with index 0 which should not occur. It causes VMD cannot load it and had a segmentation fault. vmd Info) Using plugin psf for structure file /home/birg/Desktop/zz.psf ERROR) Error reading bond information. Segmentation fault I wonder am I getting the right top2psf.pl. Or is there any place I can get the latest stable version of that script? There is only one version. Zeros are only printed if something goes wrong, i.e. you have provided the wrong input or something else has failed. Based solely on the information you've provided I cannot diagnose what has gone wrong. -Justin Here, I attached the perl script I used. Thanks. Regards, Joyce -- 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 mailto:gmx-users@gromacs.org mailto: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 mailto: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 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] top2psf.pl is generating some bonds to atoms with index 0.
Hi, I've got a top2psf.pl script from the web and used it to generate a psf file. Yet it generated some bonds to atoms with index 0 which should not occur. It causes VMD cannot load it and had a segmentation fault. vmd Info) Using plugin psf for structure file /home/birg/Desktop/zz.psf ERROR) Error reading bond information. Segmentation fault I wonder am I getting the right top2psf.pl. Or is there any place I can get the latest stable version of that script? Here, I attached the perl script I used. Thanks. Regards, Joyce top2psf.pl Description: Binary data -- 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] top2psf.pl is generating some bonds to atoms with index 0.
Kwee Hong wrote: Hi, I've got a top2psf.pl script from the web and used it to generate a psf file. Yet it generated some bonds to atoms with index 0 which should not occur. It causes VMD cannot load it and had a segmentation fault. vmd Info) Using plugin psf for structure file /home/birg/Desktop/zz.psf ERROR) Error reading bond information. Segmentation fault I wonder am I getting the right top2psf.pl. Or is there any place I can get the latest stable version of that script? There is only one version. Zeros are only printed if something goes wrong, i.e. you have provided the wrong input or something else has failed. Based solely on the information you've provided I cannot diagnose what has gone wrong. -Justin Here, I attached the perl script I used. Thanks. Regards, Joyce -- 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] top2psf.pl is generating some bonds to atoms with index 0.
Kwee Hong wrote: I executed the script at the therminal by typing perl top2psf.pl -i topol.top -o zz.psf Here, I attached my input file. Your topology does not correspond to a MARTINI coarse-grained topology. As such, probably a bunch of the pattern matching is getting incorrect information. You cannot use top2psf.pl with this type of topology. It was created for a very specific purpose and requires that format, nothing else. -Justin *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Wednesday, October 20, 2010 2:14:34 *Subject:* Re: [gmx-users] top2psf.pl is generating some bonds to atoms with index 0. Kwee Hong wrote: Hi, I've got a top2psf.pl script from the web and used it to generate a psf file. Yet it generated some bonds to atoms with index 0 which should not occur. It causes VMD cannot load it and had a segmentation fault. vmd Info) Using plugin psf for structure file /home/birg/Desktop/zz.psf ERROR) Error reading bond information. Segmentation fault I wonder am I getting the right top2psf.pl. Or is there any place I can get the latest stable version of that script? There is only one version. Zeros are only printed if something goes wrong, i.e. you have provided the wrong input or something else has failed. Based solely on the information you've provided I cannot diagnose what has gone wrong. -Justin Here, I attached the perl script I used. Thanks. Regards, Joyce -- 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 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
