Re: [gmx-users] Free energy calculation by MM_PBSA
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.
Re: [gmx-users] Free energy calculation by MM_PBSA
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.
[gmx-users] Free energy calculation by MM_PBSA
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.
Re: [gmx-users] Free energy calculation by MM_PBSA
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.
