Thank you, I have noticed this in the output of the g_saltbr. Later I separated the files according to what ever I require. My worry was only that of the dimeric interface which could not be seen because it is separated.
I will try by giving a separate tpr file without water. Thank you Kavya On Thu, Feb 7, 2013 at 5:31 PM, Justin Lemkul <[email protected]> wrote: > > > On 2/7/13 6:42 AM, Kavyashree M wrote: > >> Dear users, >> >> After simulation dimers appear separated, I was >> able to do saltbridge calculation on this. This will >> be different than doing it on a dimer which are together. >> Am I correct? >> >> > Most Gromacs tools handle PBC well for simple metrics like measurements. > I would suspect that the seg fault comes from a mismatch in the .tpr and > .xtc contents. g_saltbr is a rather stupid tool that tries to guess salt > bridges based on anything that's charged, which includes ions and other > groups that don't necessarily participate in such interactions (see the > discussion on this same topic in recent days). Perhaps if g_saltbr is > identifying elements that it wants to examine from the .tpr file but can't > find them in the trajectory, you get a seg fault. This shouldn't happen, > but you can also use tpbconv to produce a subset .tpr file with just the > protein for the purposes of analysis. > > -Justin > > > On Thu, Feb 7, 2013 at 3:39 PM, Kavyashree M <[email protected]> wrote: >> >> Dear users, >>> >>> While calculating salt bridges using g_saltbr I got >>> segmentation fault when I used trajectory with only >>> the protein. But when I used the trajectory with >>> water It worked. But the problem was that the >>> monomers were far apart in the trajectory with water >>> and not with the only-protein trajectory. >>> >>> Kindly help! >>> >>> Thank you >>> Kavya >>> >>> >>> > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to [email protected]. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
