On 7/14/14, 7:44 AM, mirko busato wrote:
Dear Users, 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 wouldn't use g_hbond like this; g_mindist -on is more straightforward for calculating simple contacts.
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 ?
Order of the groups in the index file is irrelevant; it doesn't seem likely that this is the only issue.
-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.
