Re: [gmx-users] Problem with g_chi options
Hi! I've just encountered exactly the same problem. I have a trajectory from another group and a .pdb-file with the reference structure. From the pdb I generated a tpr file, however g_chi finishes with these infos: '57 residues with dihedrals found 276 dihedrals found Reading frame 1514000 time 75667.297 j after resetting (nr. active dihedrals) = 170 WARNING: not all dihedrals found in topology (only 170 out of 276)!' This suggests, that it can only find the backbone dihedrals, but not the ones of the sidechains. I do not get, what is meant by 'active dihedrals'. Additionally, if g_chi relies on topological information from a tpr-like file, we should perhaps change this help '-s conf.gro InputStructure file: gro g96 pdb tpr etc.' (like in g_rama). Any little hints to this problem are highly welcome. Cheers, Florian On 07/14/2014 04:33 PM, Anna Stopka wrote: Hi! Thanks for your reply Justin! I have tried using a tpr file instead of a gro file, but that makes no difference. I still have the same problem! Does anybody have another idea? Thanks in advance! Anna On 07/09/2014 07:24 PM, Justin Lemkul wrote: On 7/9/14, 5:51 AM, Anna Stopka wrote: Hi everybody, I wrote last week, but nobody answered. So I write again, still having the same problem: I want do an analysis of my simulation with the tool g_chi. The problem is, that the optional output options don't work. I use the following command: g_chi -s config.gro -f traj.xtc -oh -all and all I get are the standard output files chi.log and order.xvg. I am not sure if it has something to do with the following warning I get: WARNING: not all dihedrals found in topology (only 1056 out of 1746)! Honestly, I don't understand why I get this warning, because all the input files are fine. Have you tried using a .tpr file instead of a .gro file as the structure passed to -s? I don't know how there can be any interpretation of a topology, given the fact that you haven't passed any topological information to g_chi. -Justin -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem with g_chi options
Hi! Thanks for your reply Justin! I have tried using a tpr file instead of a gro file, but that makes no difference. I still have the same problem! Does anybody have another idea? Thanks in advance! Anna On 07/09/2014 07:24 PM, Justin Lemkul wrote: On 7/9/14, 5:51 AM, Anna Stopka wrote: Hi everybody, I wrote last week, but nobody answered. So I write again, still having the same problem: I want do an analysis of my simulation with the tool g_chi. The problem is, that the optional output options don't work. I use the following command: g_chi -s config.gro -f traj.xtc -oh -all and all I get are the standard output files chi.log and order.xvg. I am not sure if it has something to do with the following warning I get: WARNING: not all dihedrals found in topology (only 1056 out of 1746)! Honestly, I don't understand why I get this warning, because all the input files are fine. Have you tried using a .tpr file instead of a .gro file as the structure passed to -s? I don't know how there can be any interpretation of a topology, given the fact that you haven't passed any topological information to g_chi. -Justin -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Problem with g_chi options
Hi everybody, I wrote last week, but nobody answered. So I write again, still having the same problem: I want do an analysis of my simulation with the tool g_chi. The problem is, that the optional output options don't work. I use the following command: g_chi -s config.gro -f traj.xtc -oh -all and all I get are the standard output files chi.log and order.xvg. I am not sure if it has something to do with the following warning I get: WARNING: not all dihedrals found in topology (only 1056 out of 1746)! Honestly, I don't understand why I get this warning, because all the input files are fine. Thanks for your help! Best regards, Anna -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem with g_chi options
On 7/9/14, 5:51 AM, Anna Stopka wrote: Hi everybody, I wrote last week, but nobody answered. So I write again, still having the same problem: I want do an analysis of my simulation with the tool g_chi. The problem is, that the optional output options don't work. I use the following command: g_chi -s config.gro -f traj.xtc -oh -all and all I get are the standard output files chi.log and order.xvg. I am not sure if it has something to do with the following warning I get: WARNING: not all dihedrals found in topology (only 1056 out of 1746)! Honestly, I don't understand why I get this warning, because all the input files are fine. Have you tried using a .tpr file instead of a .gro file as the structure passed to -s? I don't know how there can be any interpretation of a topology, given the fact that you haven't passed any topological information to g_chi. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Problem with g_chi options
Hi, I want do an analysis of my simulation with the tool g_chi. The problem is, that the optional output options don't work. I use the following command: g_chi -s config.gro -f traj.xtc -oh -all and all I get are the standard output files chi.log and order.xvg. I am not sure if it has something to do with the following warning I get: WARNING: not all dihedrals found in topology (only 1056 out of 1746)! Honestly, I don't understand why I get this warning, because all the input files are fine. Thanks for your help! Best regards, Anna -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
