Sarah Witzke wrote: > Dear gmx users, > > > > I'm sorry to continue an old thread - here's a summary: > > I have a DMPC bilayer surrounded by water and a small organic molecule with a > deprotonated carboxylic acid. The small molecule diffuses near the membrane > interface/into the membrane. I would like to calculate any formed salt bridge > between the negative carboxylic acid of the small molecule and the positive > charge of the DMPC choline nitrogen. To do this I use these two commands: > > g_saltbr -f zzz.xtc -s zzz.tpr -t 0.5 -b 100000 > > g_saltbr -f zzz.xtc -s zzz.tpr -t 0.5 -b 100000 -sep > > The first command I use to get the files min-min.xvg, plus-plus.xvg and > plus-min.xvg. Here I am interested in plus-min.xvg to tell me which of the > salt bridges between the small molecule and DMPC is between the negative acid > and the positive choline (as opposed to between the negative acid and the > negative phosphate of DMPC). > > Then I run the command again with -sep to get the individual graphs of each > interaction. This is unfortunately a rather tedious exercise since very many > files are generated for all sort of charged interactions (DMPC-DMPC, > smallmolecule-smallmolecule, counterion-counterion, and pairs thereof), and > then I have to select the wanted ones by looking through plus-min.xvg. I > guess I could make some sort of script to make it easier, but I just want to > check if there is absolutely no way to include an .ndx file or only choose > plus-min interactions? >
Per the documentation, the only options that can be passed to g_saltbr are -s and -f, so no, you cannot use any index groups. I thought so :-( > > > Another thing, when running the second command several of each files are > generated, for instance: > > sb-DMPC144:DMPC154.xvg > > #sb-DMPC144:DMPC154.xvg.3# > > Etc > > The files are not identical when checked with "diff" or looked at in xmgrace. > > > I suppose the last generated files are the "correct" one, but what are all > the other files? > Previous attempts at running the command generate backups. These sb-*.xvg files only come from using the -sep option, so issuing only the two commands above would not generate any backups (the ones that are flanked by #). Have you run different g_saltbr commands in the same directory? Perhaps using different values of -b and/or -t? There are no old xvg files in the directory. I have used "rm -rf *xvg*" to clean up and checked with "ls -alt". Just now I also ran the command in a folder that I have not analyzed before - with the same huge amount og #-files. Also note the dates of the files are within minutes, eg.: -rw-r--r-- 1 sawit02 users 699 2009-12-02 00:56 sb-DMPC191:DMPC192.xvg -rw-r--r-- 1 sawit02 users 699 2009-12-02 00:56 #sb-DMPC191:DMPC192.xvg.1# -rw-r--r-- 1 sawit02 users 699 2009-12-02 00:56 #sb-DMPC191:DMPC192.xvg.2# -rw-r--r-- 1 sawit02 users 699 2009-12-02 00:56 #sb-DMPC191:DMPC192.xvg.3# -Justin -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php