Re: [gmx-users] frequency of contact between all residue pairs
Hi Erik, Thank you for the suggestion. But, will this not only give me H-bond contacts only? I am looking for any contact. The only way I can see to make this work is to make all atoms donors and acceptors, and I do not know how to do this. Am I missing something or is there a simple way to do this? Thanks so much. -Dina On Wed, Oct 21, 2015 at 11:09 AM, Erik Marklund <erik.markl...@chem.ox.ac.uk > wrote: > Hi Dina, > > g_hbond -contact -hbn -hbm, then post-process the resulting contact matrix > to represent residue-residue interactions. > > Kind regards, > Erik > > Erik Marklund, PhD > Postdoctoral Research Fellow > Fulford JRF, Somerville College > > Department of Chemistry > Physical & Theoretical Chemistry Laboratory > University of Oxford > South Parks Road > Oxford > OX1 3QZ > > > On 21 Oct 2015, at 15:56, Dina Mirijanian <dmi...@brandeis.edu> wrote: > > > > Hello, > > > > I need to calculate the contact frequence between all pairs of residues > in > > my protein within a certain cutoff. I was trying to figure out a way to > do > > this with g_mindist. But I have not been able to get it do what I want. > > Can someone tell me what is the best way to calculate the contact > frequence > > between all residues from a trajectory? > > Thank you so much. > > -Dina > > -- > > 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. > > -- > 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. > -- 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] frequency of contact between all residue pairs
Hello, I need to calculate the contact frequence between all pairs of residues in my protein within a certain cutoff. I was trying to figure out a way to do this with g_mindist. But I have not been able to get it do what I want. Can someone tell me what is the best way to calculate the contact frequence between all residues from a trajectory? Thank you so much. -Dina -- 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] g_chi Segmentation fault for -maxchi greater than 3
I found that with an older version g_chi works fine for the system. Thanks for your help. On Thu, Aug 27, 2015 at 9:15 PM, Dina Mirijanian dmi...@brandeis.edu wrote: No. I have ARG and LYS residues. And I checked the protein trajectory after trjconv and these residues seemed to be whole. On Thursday, August 27, 2015, Justin Lemkul jalem...@vt.edu wrote: On 8/27/15 12:33 PM, Dina Mirijanian wrote: Hello, I have done a simulation of two protein segments in water and ions. I have processed my trajectory from the simulation with trjconv using the flag -pbc whole in order to make all the bonds whole again, lets call the output trajectory from this prot_whole.xtc. I then run g_chi -s protein_whole.pdb -f prot_whole.xtc -all -maxchi 6 to get the files with all the dihedrals. I get the following writeout before it crashes: 257 residues with dihedrals found 1184 dihedrals found Reading frame 13000 time 325000.000 Segmentation fault (core dumped) However when I run the same g_chi command line with -maxchi 1 it runs fine and writes out the .xvg files with the dihedrals: 257 residues with dihedrals found 1184 dihedrals found Reading frame 13000 time 325000.000 j after resetting (nr. active dihedrals) = 983 Printing chi1VAL20.xvg The g_chi command works fine for -maxchi 1,2,3 but gives a Segmentation fault for -maxchi 4,5,6. I'm having a hard time figuring out what the problem is. Has anyone ever run into this problem? I am using gromacs 5.0.5 Probably your structure doesn't have any residues with 3 chi torsions. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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. -- 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] g_chi Segmentation fault for -maxchi greater than 3
OK. WIll do. For FYI here are the versions I tested and the version that worked: GROMACS/5.0.6NO GROMACS/5.0.5NO GROMACS/5.0.4NO GROMACS/4.6.3NO GROMACS/4.5.5YES! On Fri, Aug 28, 2015 at 11:33 AM, Justin Lemkul jalem...@vt.edu wrote: On 8/28/15 11:30 AM, Dina Mirijanian wrote: I found that with an older version g_chi works fine for the system. Thanks for your help. Then we clearly have a bug that needs to be fixed. If you would, please upload a test case (.tpr and a single coordinate file should do it) to redmine.gromacs.org with your command line and/or link to this thread. -Justin On Thu, Aug 27, 2015 at 9:15 PM, Dina Mirijanian dmi...@brandeis.edu wrote: No. I have ARG and LYS residues. And I checked the protein trajectory after trjconv and these residues seemed to be whole. On Thursday, August 27, 2015, Justin Lemkul jalem...@vt.edu wrote: On 8/27/15 12:33 PM, Dina Mirijanian wrote: Hello, I have done a simulation of two protein segments in water and ions. I have processed my trajectory from the simulation with trjconv using the flag -pbc whole in order to make all the bonds whole again, lets call the output trajectory from this prot_whole.xtc. I then run g_chi -s protein_whole.pdb -f prot_whole.xtc -all -maxchi 6 to get the files with all the dihedrals. I get the following writeout before it crashes: 257 residues with dihedrals found 1184 dihedrals found Reading frame 13000 time 325000.000 Segmentation fault (core dumped) However when I run the same g_chi command line with -maxchi 1 it runs fine and writes out the .xvg files with the dihedrals: 257 residues with dihedrals found 1184 dihedrals found Reading frame 13000 time 325000.000 j after resetting (nr. active dihedrals) = 983 Printing chi1VAL20.xvg The g_chi command works fine for -maxchi 1,2,3 but gives a Segmentation fault for -maxchi 4,5,6. I'm having a hard time figuring out what the problem is. Has anyone ever run into this problem? I am using gromacs 5.0.5 Probably your structure doesn't have any residues with 3 chi torsions. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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. -- 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] g_chi Segmentation fault for -maxchi greater than 3
Hello, I have done a simulation of two protein segments in water and ions. I have processed my trajectory from the simulation with trjconv using the flag -pbc whole in order to make all the bonds whole again, lets call the output trajectory from this prot_whole.xtc. I then run g_chi -s protein_whole.pdb -f prot_whole.xtc -all -maxchi 6 to get the files with all the dihedrals. I get the following writeout before it crashes: 257 residues with dihedrals found 1184 dihedrals found Reading frame 13000 time 325000.000 Segmentation fault (core dumped) However when I run the same g_chi command line with -maxchi 1 it runs fine and writes out the .xvg files with the dihedrals: 257 residues with dihedrals found 1184 dihedrals found Reading frame 13000 time 325000.000 j after resetting (nr. active dihedrals) = 983 Printing chi1VAL20.xvg The g_chi command works fine for -maxchi 1,2,3 but gives a Segmentation fault for -maxchi 4,5,6. I'm having a hard time figuring out what the problem is. Has anyone ever run into this problem? I am using gromacs 5.0.5 Thank you very much. -Dina -- 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] g_chi Segmentation fault for -maxchi greater than 3
No. I have ARG and LYS residues. And I checked the protein trajectory after trjconv and these residues seemed to be whole. On Thursday, August 27, 2015, Justin Lemkul jalem...@vt.edu wrote: On 8/27/15 12:33 PM, Dina Mirijanian wrote: Hello, I have done a simulation of two protein segments in water and ions. I have processed my trajectory from the simulation with trjconv using the flag -pbc whole in order to make all the bonds whole again, lets call the output trajectory from this prot_whole.xtc. I then run g_chi -s protein_whole.pdb -f prot_whole.xtc -all -maxchi 6 to get the files with all the dihedrals. I get the following writeout before it crashes: 257 residues with dihedrals found 1184 dihedrals found Reading frame 13000 time 325000.000 Segmentation fault (core dumped) However when I run the same g_chi command line with -maxchi 1 it runs fine and writes out the .xvg files with the dihedrals: 257 residues with dihedrals found 1184 dihedrals found Reading frame 13000 time 325000.000 j after resetting (nr. active dihedrals) = 983 Printing chi1VAL20.xvg The g_chi command works fine for -maxchi 1,2,3 but gives a Segmentation fault for -maxchi 4,5,6. I'm having a hard time figuring out what the problem is. Has anyone ever run into this problem? I am using gromacs 5.0.5 Probably your structure doesn't have any residues with 3 chi torsions. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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. -- 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.
