Re: [gmx-users] .top file from .tpr and .xtc
Hi, if you were able to obtain a simulation it means you had a valid .top file! In any case, gromacs recognises disulfide basing on the distance beween the SG atoms. In addition, the two chains are supposed to be in the same molecule. So, my advice is, remove all the TER from pdb (but the last one), leave the chain id and use pdb2gmx with the option -chainsep ter. The result is supposed to be a topology where your chain are grouped in a single molecule,making possible to create the bridge, and at the same time you keep the chain name for future analysis. Francesco 2013/3/19 shahid nayeem msnay...@gmail.com Hi To be more clear I have .xtc file for a disulfide linked complex of two chains. From this trajectory I can extract .xtc file for individual chains. But when I generate .top file from individual chain pdb I get one atom extra in .top file i.e. protonated SG of Cys which I dont need in order to make my .xtc and .top file compatible. Shahid On Tue, Mar 19, 2013 at 2:07 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/18/13 12:35 PM, shahid nayeem wrote: Hi Is it possible to write .top file from .xtc and .tpr using index.ndx so that .top is available for tailormade components of simulated protein. All topology information is in the .tpr, but not in .top format. You may be able to post-process the output of gmxdump to produce some hacked version, but that's just a bit of a hand-waving guess. I don't really understand what your objective is. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 -- Cordiali saluti, Dr.Oteri Francesco -- 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] .top file from .tpr and .xtc
Thanks Francesco. But my problem is exactly opposite. I do have a .top file containing both chain linked by disulfide bridge. I ran the simulation. Now I have extracted .xtc file for each chain separately and I want the corresponding, separate .top file for each chain. when I separate the pdb and run the pdb2gmx I get one hydrogen on SG atom of Cys which is absent in .xtc file. So the .top file generated this way has one atom more as compared to .xtc file. shahid On Tue, Mar 19, 2013 at 1:07 PM, francesco oteri francesco.ot...@gmail.com wrote: Hi, if you were able to obtain a simulation it means you had a valid .top file! In any case, gromacs recognises disulfide basing on the distance beween the SG atoms. In addition, the two chains are supposed to be in the same molecule. So, my advice is, remove all the TER from pdb (but the last one), leave the chain id and use pdb2gmx with the option -chainsep ter. The result is supposed to be a topology where your chain are grouped in a single molecule,making possible to create the bridge, and at the same time you keep the chain name for future analysis. Francesco 2013/3/19 shahid nayeem msnay...@gmail.com Hi To be more clear I have .xtc file for a disulfide linked complex of two chains. From this trajectory I can extract .xtc file for individual chains. But when I generate .top file from individual chain pdb I get one atom extra in .top file i.e. protonated SG of Cys which I dont need in order to make my .xtc and .top file compatible. Shahid On Tue, Mar 19, 2013 at 2:07 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/18/13 12:35 PM, shahid nayeem wrote: Hi Is it possible to write .top file from .xtc and .tpr using index.ndx so that .top is available for tailormade components of simulated protein. All topology information is in the .tpr, but not in .top format. You may be able to post-process the output of gmxdump to produce some hacked version, but that's just a bit of a hand-waving guess. I don't really understand what your objective is. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 -- Cordiali saluti, Dr.Oteri Francesco -- 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] .top file from .tpr and .xtc
Could you simply edit the file and removing the atom from [atoms] section ? grompp wil complain regarding the line containing interactions. But also these few lines can be removed. Otherwise, vmd has the TopoTools that write the .top topology of the loaded pdb. Unfortunately, this topologyes are not useful for carrying out MD because they lack parameters. In any case are good for analysis! Francesco 2013/3/19 shahid nayeem msnay...@gmail.com Thanks Francesco. But my problem is exactly opposite. I do have a .top file containing both chain linked by disulfide bridge. I ran the simulation. Now I have extracted .xtc file for each chain separately and I want the corresponding, separate .top file for each chain. when I separate the pdb and run the pdb2gmx I get one hydrogen on SG atom of Cys which is absent in .xtc file. So the .top file generated this way has one atom more as compared to .xtc file. shahid On Tue, Mar 19, 2013 at 1:07 PM, francesco oteri francesco.ot...@gmail.com wrote: Hi, if you were able to obtain a simulation it means you had a valid .top file! In any case, gromacs recognises disulfide basing on the distance beween the SG atoms. In addition, the two chains are supposed to be in the same molecule. So, my advice is, remove all the TER from pdb (but the last one), leave the chain id and use pdb2gmx with the option -chainsep ter. The result is supposed to be a topology where your chain are grouped in a single molecule,making possible to create the bridge, and at the same time you keep the chain name for future analysis. Francesco 2013/3/19 shahid nayeem msnay...@gmail.com Hi To be more clear I have .xtc file for a disulfide linked complex of two chains. From this trajectory I can extract .xtc file for individual chains. But when I generate .top file from individual chain pdb I get one atom extra in .top file i.e. protonated SG of Cys which I dont need in order to make my .xtc and .top file compatible. Shahid On Tue, Mar 19, 2013 at 2:07 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/18/13 12:35 PM, shahid nayeem wrote: Hi Is it possible to write .top file from .xtc and .tpr using index.ndx so that .top is available for tailormade components of simulated protein. All topology information is in the .tpr, but not in .top format. You may be able to post-process the output of gmxdump to produce some hacked version, but that's just a bit of a hand-waving guess. I don't really understand what your objective is. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 -- Cordiali saluti, Dr.Oteri Francesco -- 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 -- Cordiali saluti, Dr.Oteri Francesco -- 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
Re: [gmx-users] .top file from .tpr and .xtc
I did it. Simply I changed the name of Cys which forms interchain dsiulfide bond to CYS2 in the separated pdb file and I used G43a1 forcefeild to run pdb2gmx. This gives a topology with same number of atom which is present in .xtc file. CYS2 is present .rtp file of G43a1 forcefeild probably to form interchain disulfide bond reading from specbond.dat. Am I right in generating such half disulfide bond topology. shahid On Tue, Mar 19, 2013 at 2:10 PM, francesco oteri francesco.ot...@gmail.com wrote: Could you simply edit the file and removing the atom from [atoms] section ? grompp wil complain regarding the line containing interactions. But also these few lines can be removed. Otherwise, vmd has the TopoTools that write the .top topology of the loaded pdb. Unfortunately, this topologyes are not useful for carrying out MD because they lack parameters. In any case are good for analysis! Francesco 2013/3/19 shahid nayeem msnay...@gmail.com Thanks Francesco. But my problem is exactly opposite. I do have a .top file containing both chain linked by disulfide bridge. I ran the simulation. Now I have extracted .xtc file for each chain separately and I want the corresponding, separate .top file for each chain. when I separate the pdb and run the pdb2gmx I get one hydrogen on SG atom of Cys which is absent in .xtc file. So the .top file generated this way has one atom more as compared to .xtc file. shahid On Tue, Mar 19, 2013 at 1:07 PM, francesco oteri francesco.ot...@gmail.com wrote: Hi, if you were able to obtain a simulation it means you had a valid .top file! In any case, gromacs recognises disulfide basing on the distance beween the SG atoms. In addition, the two chains are supposed to be in the same molecule. So, my advice is, remove all the TER from pdb (but the last one), leave the chain id and use pdb2gmx with the option -chainsep ter. The result is supposed to be a topology where your chain are grouped in a single molecule,making possible to create the bridge, and at the same time you keep the chain name for future analysis. Francesco 2013/3/19 shahid nayeem msnay...@gmail.com Hi To be more clear I have .xtc file for a disulfide linked complex of two chains. From this trajectory I can extract .xtc file for individual chains. But when I generate .top file from individual chain pdb I get one atom extra in .top file i.e. protonated SG of Cys which I dont need in order to make my .xtc and .top file compatible. Shahid On Tue, Mar 19, 2013 at 2:07 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/18/13 12:35 PM, shahid nayeem wrote: Hi Is it possible to write .top file from .xtc and .tpr using index.ndx so that .top is available for tailormade components of simulated protein. All topology information is in the .tpr, but not in .top format. You may be able to post-process the output of gmxdump to produce some hacked version, but that's just a bit of a hand-waving guess. I don't really understand what your objective is. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 -- Cordiali saluti, Dr.Oteri Francesco -- 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
Re: [gmx-users] .top file from .tpr and .xtc
If it works then you are right :) 2013/3/19 shahid nayeem msnay...@gmail.com I did it. Simply I changed the name of Cys which forms interchain dsiulfide bond to CYS2 in the separated pdb file and I used G43a1 forcefeild to run pdb2gmx. This gives a topology with same number of atom which is present in .xtc file. CYS2 is present .rtp file of G43a1 forcefeild probably to form interchain disulfide bond reading from specbond.dat. Am I right in generating such half disulfide bond topology. shahid On Tue, Mar 19, 2013 at 2:10 PM, francesco oteri francesco.ot...@gmail.com wrote: Could you simply edit the file and removing the atom from [atoms] section ? grompp wil complain regarding the line containing interactions. But also these few lines can be removed. Otherwise, vmd has the TopoTools that write the .top topology of the loaded pdb. Unfortunately, this topologyes are not useful for carrying out MD because they lack parameters. In any case are good for analysis! Francesco 2013/3/19 shahid nayeem msnay...@gmail.com Thanks Francesco. But my problem is exactly opposite. I do have a .top file containing both chain linked by disulfide bridge. I ran the simulation. Now I have extracted .xtc file for each chain separately and I want the corresponding, separate .top file for each chain. when I separate the pdb and run the pdb2gmx I get one hydrogen on SG atom of Cys which is absent in .xtc file. So the .top file generated this way has one atom more as compared to .xtc file. shahid On Tue, Mar 19, 2013 at 1:07 PM, francesco oteri francesco.ot...@gmail.com wrote: Hi, if you were able to obtain a simulation it means you had a valid .top file! In any case, gromacs recognises disulfide basing on the distance beween the SG atoms. In addition, the two chains are supposed to be in the same molecule. So, my advice is, remove all the TER from pdb (but the last one), leave the chain id and use pdb2gmx with the option -chainsep ter. The result is supposed to be a topology where your chain are grouped in a single molecule,making possible to create the bridge, and at the same time you keep the chain name for future analysis. Francesco 2013/3/19 shahid nayeem msnay...@gmail.com Hi To be more clear I have .xtc file for a disulfide linked complex of two chains. From this trajectory I can extract .xtc file for individual chains. But when I generate .top file from individual chain pdb I get one atom extra in .top file i.e. protonated SG of Cys which I dont need in order to make my .xtc and .top file compatible. Shahid On Tue, Mar 19, 2013 at 2:07 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/18/13 12:35 PM, shahid nayeem wrote: Hi Is it possible to write .top file from .xtc and .tpr using index.ndx so that .top is available for tailormade components of simulated protein. All topology information is in the .tpr, but not in .top format. You may be able to post-process the output of gmxdump to produce some hacked version, but that's just a bit of a hand-waving guess. I don't really understand what your objective is. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 -- Cordiali saluti, Dr.Oteri Francesco -- 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
Re: [gmx-users] .top file from .tpr and .xtc
On 3/18/13 12:35 PM, shahid nayeem wrote: Hi Is it possible to write .top file from .xtc and .tpr using index.ndx so that .top is available for tailormade components of simulated protein. All topology information is in the .tpr, but not in .top format. You may be able to post-process the output of gmxdump to produce some hacked version, but that's just a bit of a hand-waving guess. I don't really understand what your objective is. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] .top file from .tpr and .xtc
Hi To be more clear I have .xtc file for a disulfide linked complex of two chains. From this trajectory I can extract .xtc file for individual chains. But when I generate .top file from individual chain pdb I get one atom extra in .top file i.e. protonated SG of Cys which I dont need in order to make my .xtc and .top file compatible. Shahid On Tue, Mar 19, 2013 at 2:07 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/18/13 12:35 PM, shahid nayeem wrote: Hi Is it possible to write .top file from .xtc and .tpr using index.ndx so that .top is available for tailormade components of simulated protein. All topology information is in the .tpr, but not in .top format. You may be able to post-process the output of gmxdump to produce some hacked version, but that's just a bit of a hand-waving guess. I don't really understand what your objective is. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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
