Re: [gmx-users] Hydrogen Bond analysis
On 10/4/19 12:11 PM, Pandya, Akash wrote: Hi all, This may sound like a stupid question, but is there a "selection process" within gromacs whereby I can determine the correct donor-acceptor distance and angle cut-offs for hydrogen bond analysis for my protein-ligand. Just glancing various literature that study protein-water/ protein-ligand/ligand-water interactions, the authors seem to use varying cut-offs e.g. 0.35/0.24 nm. I know 0.35 nm is used for moderate hydrogen bond and 0.24 nm is a strong hydrogen bond. So basically what I am asking is how do I find the optimum cut-off values? Do I simply use trial and error? Or can I used other gromacs utilities such as gmx gangle and distance to help me make a decision? The distinction between 0.35 and 0.24 nm is probably whether the H-bond is defined using the donor atom or the hydrogen itself, respectively. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] Hydrogen Bond analysis
Hi all, This may sound like a stupid question, but is there a "selection process" within gromacs whereby I can determine the correct donor-acceptor distance and angle cut-offs for hydrogen bond analysis for my protein-ligand. Just glancing various literature that study protein-water/ protein-ligand/ligand-water interactions, the authors seem to use varying cut-offs e.g. 0.35/0.24 nm. I know 0.35 nm is used for moderate hydrogen bond and 0.24 nm is a strong hydrogen bond. So basically what I am asking is how do I find the optimum cut-off values? Do I simply use trial and error? Or can I used other gromacs utilities such as gmx gangle and distance to help me make a decision? Akash -- 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] Hydrogen bond analysis
Hi allI want to carry on a hydrogen bond analysis between a protein and ligand. I tested hbond but it only gives the number of hydrogen bonds which I am not looking for. I want to know exactly which residues are involved in hydrogen bonding and more specifically which atoms of the residues and ligand have interaction during the whole simulation time.Any help would be appreciated!Thank you. -- 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] hydrogen bond analysis
On 6/19/17 3:49 AM, João Henriques wrote: Dear Imrul, I believe the information you seek is right there in your xvg file header: @xaxis label "Time (ns)" @yaxis label "Number" ... @ s0 legend "Hydrogen bonds" @ s1 legend "Pairs within 0.35 nm" First column is always time (x-axis). All other columns are y-axes for different properties (in this case you two, s0 and s1). s0 is clearly stated as being hydrogen bonds and s1 as pairs within 0.35 nm. Just to add on: pairs within 0.35 nm are pairs of atoms that satisfy the hydrogen bonding distance criterion, but not the angle. The two columns in the output file are mutually exclusive (see lots of discussion from last week on this same topic). -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.
Re: [gmx-users] hydrogen bond analysis
Dear Imrul, I believe the information you seek is right there in your xvg file header: @xaxis label "Time (ns)" @yaxis label "Number" ... @ s0 legend "Hydrogen bonds" @ s1 legend "Pairs within 0.35 nm" First column is always time (x-axis). All other columns are y-axes for different properties (in this case you two, s0 and s1). s0 is clearly stated as being hydrogen bonds and s1 as pairs within 0.35 nm. Best regards, João On Mon, Jun 19, 2017 at 6:25 AM, Md. Imrul Reza Shishir < imrul.reza.shis...@gmail.com> wrote: > Dear all > For hydrogen bond analysis, we generate *.xvg file for -num tag in gmx > hbond command. My inquiry is in the xvg file there are three column > output. First column is time. Which one is hydrogen bond number? > If number 2 column is hydrogen bond number in every frame than what is > number 3 column. > "" > @title "Hydrogen Bonds" > @xaxis label "Time (ns)" > @yaxis label "Number" > @TYPE xy > @ view 0.15, 0.15, 0.75, 0.85 > @ legend on > @ legend box on > @ legend loctype view > @ legend 0.78, 0.8 > @ legend length 2 > @ s0 legend "Hydrogen bonds" > @ s1 legend "Pairs within 0.35 nm" > 0 7 11 > 0.001 8 10 > 0.002 7 11 > 0.003 6 12 > 0.004 7 11 > "" > Thank you very much in advanced. > > Best Regards. > > -- > *Md Imrul Reza Shishir* > Master Student > *Inha University* > -- > 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] hydrogen bond analysis
Dear all For hydrogen bond analysis, we generate *.xvg file for -num tag in gmx hbond command. My inquiry is in the xvg file there are three column output. First column is time. Which one is hydrogen bond number? If number 2 column is hydrogen bond number in every frame than what is number 3 column. "" @title "Hydrogen Bonds" @xaxis label "Time (ns)" @yaxis label "Number" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "Hydrogen bonds" @ s1 legend "Pairs within 0.35 nm" 0 7 11 0.001 8 10 0.002 7 11 0.003 6 12 0.004 7 11 "" Thank you very much in advanced. Best Regards. -- *Md Imrul Reza Shishir* Master Student *Inha University* -- 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] hydrogen bond analysis
Dear all I wish to analyze hydrogen bonds in a gromacs MD trajectories with g_hbond. I want to get information about the life time of individual hbonds between the receptor and ligand in the structure through the trajector. in the output log file of g_hbond command, I can find the list of individual hbonds. But by using what option can I get the life time of each of these hbonds? I cannot the -life option provides a list as following: 10.000 2.399e-02 2.399e-01 30.000 8.837e-03 2.651e-01 50.000 4.897e-03 2.448e-01 70.000 2.525e-03 1.767e-01 90.000 2.219e-03 1.997e-01 110.000 1.760e-03 1.936e-01 130.000 1.033e-03 1.343e-01 150.000 7.651e-04 1.148e-01...But I don't know what does these mean. Could you help me with that? Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- 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.
