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.
