Hello, I performed 20ns MD simulations on Protein-Ligand Complex. Now i tried to analysis this complex using g_gyrate.
Used following command g_gyrate -s MD_first10.tpr -f File.xtc -n index.ndx -o ligand.xvg I Choose Ligand group but it gives this following error.. *** glibc detected *** g_gyrate: munmap_chunk(): invalid pointer: 0x0000000000b34140 *** ======= Backtrace: ========= /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7fdbb9e84b96] /usr/lib/libgmx.so.6(done_graph+0x35)[0x7fdbb96f25d5] /usr/lib/libgmx.so.6(gmx_rmpbc_done+0x36)[0x7fdbb96aa436] /usr/lib/libgmxana.so.6(gmx_gyrate+0xd0c)[0x7fdbba25000c] g_gyrate(main+0x9)[0x400629] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7fdbb9e2776d] g_gyrate[0x400659] ======= Memory map: ======== 00400000-00401000 r-xp 00000000 08:02 939978 /usr/bin/g_gyrate 00600000-00601000 r--p 00000000 08:02 939978 /usr/bin/g_gyrate 00601000-00602000 rw-p 00001000 08:02 939978 /usr/bin/g_gyrate 00b05000-00c5f000 rw-p 00000000 00:00 0 [heap] 7fdbb7d56000-7fdbb7d6b000 r-xp 00000000 08:02 2354732 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fdbb7d6b000-7fdbb7f6a000 ---p 00015000 08:02 2354732 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fdbb7f6a000-7fdbb7f6b000 r--p 00014000 08:02 2354732 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fdbb7f6b000-7fdbb7f6c000 rw-p 00015000 08:02 2354732 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fdbb7f6c000-7fdbb80b0000 rw-p 00000000 00:00 0 7fdbb80b1000-7fdbb8153000 rw-p 00000000 00:00 0 7fdbb818c000-7fdbb8193000 rw-p 00000000 00:00 0 7fdbb81f4000-7fdbb85a3000 rw-p 00000000 00:00 0 7fdbb85a3000-7fdbb867c000 rw-p 00000000 00:00 0 7fdbb867c000-7fdbb8692000 r-xp 00000000 08:02 2354831 /lib/x86_64-linux-gnu/libz.so.1.2.3.4 7fdbb8692000-7fdbb8891000 ---p 00016000 08:02 2354831 /lib/x86_64-linux-gnu/libz.so.1.2.3.4 7fdbb8891000-7fdbb8892000 r--p 00015000 08:02 2354831 /lib/x86_64-linux-gnu/libz.so.1.2.3.4 7fdbb8892000-7fdbb8893000 rw-p 00016000 08:02 2354831 /lib/x86_64-linux-gnu/libz.so.1.2.3.4 7fdbb8893000-7fdbb8895000 r-xp 00000000 08:02 2354860 /lib/x86_64-linux-gnu/libdl-2.15.so 7fdbb8895000-7fdbb8a95000 ---p 00002000 08:02 2354860 /lib/x86_64-linux-gnu/libdl-2.15.so 7fdbb8a95000-7fdbb8a96000 r--p 00002000 08:02 2354860 /lib/x86_64-linux-gnu/libdl-2.15.so 7fdbb8a96000-7fdbb8a97000 rw-p 00003000 08:02 2354860 /lib/x86_64-linux-gnu/libdl-2.15.so 7fdbb8a97000-7fdbb8be8000 r-xp 00000000 08:02 1048574 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8 7fdbb8be8000-7fdbb8de8000 ---p 00151000 08:02 1048574 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8 7fdbb8de8000-7fdbb8df0000 r--p 00151000 08:02 1048574 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8 7fdbb8df0000-7fdbb8df2000 rw-p 00159000 08:02 1048574 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8 7fdbb8df2000-7fdbb8df3000 rw-p 00000000 00:00 0 7fdbb8df3000-7fdbb8f57000 r-xp 00000000 08:02 1053298 /usr/lib/libfftw3f.so.3.3.0 7fdbb8f57000-7fdbb9156000 ---p 00164000 08:02 1053298 /usr/lib/libfftw3f.so.3.3.0 7fdbb9156000-7fdbb9162000 r--p 00163000 08:02 1053298 /usr/lib/libfftw3f.so.3.3.0 7fdbb9162000-7fdbb9163000 rw-p 0016f000 08:02 1053298 /usr/lib/libfftw3f.so.3.3.0 7fdbb9163000-7fdbb925e000 r-xp 00000000 08:02 2355059 /lib/x86_64-linux-gnu/libm-2.15.so 7fdbb925e000-7fdbb945d000 ---p 000fb000 08:02 2355059 /lib/x86_64-linux-gnu/libm-2.15.so 7fdbb945d000-7fdbb945e000 r--p 000fa000 08:02 2355059 /lib/x86_64-linux-gnu/libm-2.15.so 7fdbb945e000-7fdbb945f000 rw-p 000fb000 08:02 2355059 /lib/x86_64-linux-gnu/libm-2.15.so 7fdbb945f000-7fdbb9477000 r-xp 00000000 08:02 2354979 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fdbb9477000-7fdbb9676000 ---p 00018000 08:02 2354979 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fdbb9676000-7fdbb9677000 r--p 00017000 08:02 2354979 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fdbb9677000-7fdbb9678000 rw-p 00018000 08:02 2354979 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fdbb9678000-7fdbb967c000 rw-p 00000000 00:00 0 7fdbb967c000-7fdbb990a000 r-xp 00000000 08:02 1046764 /usr/lib/libgmx.so.6 7fdbb990a000-7fdbb9b09000 ---p 0028e000 08:02 1046764 /usr/lib/libgmx.so.6 7fdbb9b09000-7fdbb9b0f000 r--p 0028d000 08:02 1046764 /usr/lib/libgmx.so.6 7fdbb9b0f000-7fdbb9b18000 rw-p 00293000 08:02 1046764 /usr/lib/libgmx.so.6 7fdbb9b18000-7fdbb9b19000 rw-p 00000000 00:00 0 7fdbb9b19000-7fdbb9c04000 r-xp 00000000 08:02 1049312 /usr/lib/libmd.so.6 7fdbb9c04000-7fdbb9e04000 ---p 000eb000 08:02 1049312 /usr/lib/libmd.so.6 7fdbb9e04000-7fdbb9e05000 r--p 000eb000 08:02 1049312 /usr/lib/libmd.so.6 7fdbb9e05000-7fdbb9e06000 rw-p 000ec000 08:02 1049312 /usr/lib/libmd.so.6 7fdbb9e06000-7fdbb9fbb000 r-xp 00000000 08:02 2354975 /lib/x86_64-linux-gnu/libc-2.15.so 7fdbb9fbb000-7fdbba1ba000 ---p 001b5000 08:02 2354975 /lib/x86_64-linux-gnu/libc-2.15.so 7fdbba1ba000-7fdbba1be000 r--p 001b4000 08:02 2354975 /lib/x86_64-linux-gnu/libc-2.15.so 7fdbba1be000-7fdbba1c0000 rw-p 001b8000 08:02 2354975 /lib/x86_64-linux-gnu/libc-2.15.so 7fdbba1c0000-7fdbba1c5000 rw-p 00000000 00:00 0 7fdbba1c5000-7fdbba349000 r-xp 00000000 08:02 1050682 /usr/lib/libgmxana.so.6 7fdbba349000-7fdbba549000 ---p 00184000 08:02 1050682 /usr/lib/libgmxana.so.6 7fdbba549000-7fdbba54a000 r--p 00184000 08:02 1050682 /usr/lib/libgmxana.so.6 7fdbba54a000-7fdbba555000 rw-p 00185000 08:02 1050682 /usr/lib/libgmxana.so.6 7fdbba555000-7fdbba557000 rw-p 00000000 00:00 0 7fdbba557000-7fdbba579000 r-xp 00000000 08:02 2355066 /lib/x86_64-linux-gnu/ld-2.15.so 7fdbba581000-7fdbba5c0000 rw-p 00000000 00:00 0 7fdbba5c0000-7fdbba5ee000 rw-p 00000000 00:00 0 7fdbba619000-7fdbba641000 rw-p 00000000 00:00 0 7fdbba684000-7fdbba758000 rw-p 00000000 00:00 0 7fdbba774000-7fdbba779000 rw-p 00000000 00:00 0 7fdbba779000-7fdbba77a000 r--p 00022000 08:02 2355066 /lib/x86_64-linux-gnu/ld-2.15.so 7fdbba77a000-7fdbba77c000 rw-p 00023000 08:02 2355066 /lib/x86_64-linux-gnu/ld-2.15.so 7fff90a8b000-7fff90aaa000 rwxp 00000000 00:00 0 [stack] 7fff90aaa000-7fff90aac000 rw-p 00000000 00:00 0 7fff90aef000-7fff90af0000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] Aborted This result gives zero. But I also choose protein group which worked perfectly.. Can anybody tell how to solve this issue Thanks, Sainitin -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
