Thank you very much, I have one question for you. I would like to extract some information about salt bridge interactions (without using the gromacs command g_saltbr because it gave me some problems) between some atoms (charged negatively) of a type of monomer and some atoms (charged positively )of another type of monomer.
So I created the two lists of atoms with g_select, and I made a file index like that: [ N_CRL ] 300 321 342 363 384 405 426 447 468 489 510 531 552 573 594 615 636 657 678 699 720 741 762 783 804 825 846 867 888 909 930 951 972 993 1014 1035 1056 1077 1098 1119 [ OX_ITA ] 168 181 194 207 220 233 246 259 272 285 and then I used g_hbond to extract the contacts of these 2 lists of atoms within 4 Å. in this way: g_hbond_d -f eq4.gro -s eq3.tpr -n index.ndx -hbn hbond.ndx -contact -r2 0.4 -r 0.4 I noticed a strange thing, if I change the order of the groups in the index.ndx file,like that: [ OX_ITA ] 168 181 194 207 220 233 246 259 272 285 [ N_CRL ] 300 321 342 363 384 405 426 447 468 489 510 531 552 573 594 615 636 657 678 699 720 741 762 783 804 825 846 867 888 909 930 951 972 993 1014 1035 1056 1077 1098 1119 I obtain no contacts, and it is wrong because actually I didn't change the atoms of the groups. Could you help me about it ? Thank you very much Mirko On Wednesday, June 25, 2014 12:00 PM, Justin Lemkul <jalem...@vt.edu> wrote: On 6/25/14, 4:44 AM, mirko busato wrote: > Thank you very much, > > In my analysis ,I would like to consider Hydrogen bonds involving S atom as > well. I think that g_hbond is not built to manage Hydrogen bonds with S. > > Do you know if there are available scripts? or Could you suggest me something > to solve this problem? > g_hbond is hard-coded to deal with certain groups, so it's not very flexible. The workaround we've used in the past is to simply rename the S atoms of interest as O in the .top file, generate a .tpr with those dummy names, and run g_hbond using that .tpr file. -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.