[gmx-users] Issue in ligand gyration analysis

[Sainitin Donakonda]

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