Hello everyone, I tried to do it for single (snapshot) .trr file, but the error is same, SEGMENTATION FAULT. I am not able to figure out problem.
With regards, Indu On Tue, Dec 9, 2014 at 1:56 PM, Indu Kumari <kumari.ind...@gmail.com> wrote: > > Thank you. > > > With regards, > Indu > > On Tue, Dec 9, 2014 at 12:59 PM, Bikash Ranjan Sahoo < > bikash.bioinformat...@gmail.com> wrote: > >> Hi, >> This usually occurred when you run apbs for a large number of >> conformations >> serially. Sometimes, a big protein (800-1000 residues) also arrested the >> program as apbs consumes a very high memory on cluster (in my case for 500 >> snapshots ~400 aa long protein it consumes ~300-400GB). Try using a small >> number of snapshots if you are running in parallel. And if you are running >> one pro, lig and complex in your local computer, kindly check the CPU >> usage >> and do the needful. Core dumped usually fired with memory inadequacy. >> >> ---------------------------------------------------------- >> *BIKASH RANJAN SAHOO * >> >> *Osaka Univ. Japan* >> >> On Tue, Dec 9, 2014 at 4:16 PM, Indu Kumari <kumari.ind...@gmail.com> >> wrote: >> >> > Hello everyone, >> > >> > I am trying to calculate free energy of protein ligand complex by using >> > MM_PBSA method. While calculating polar solvation energy of the >> complex, I >> > am getting this error. >> > >> > * Segmentation fault (core dumped).* >> > >> > *Please help!* >> > With regards, >> > Indu >> > -- >> > 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. >> > > -- 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.
