[gmx-users] Issue in ligand gyration analysis

Justin Lemkul jalemkul at vt.edu
Fri Aug 23 15:12:02 CEST 2013 


On 8/23/13 3:25 AM, Sainitin Donakonda wrote:
> 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
>

Looks like a bug.  Radii of gyration are usually calculated for larger 
molecules, so I don't know what value the Rg of a ligand will be.  Feel free to 
submit a bug report on redmine.gromacs.org with a minimal test case (i.e. .tpr + 
.gro) to reproduce the issue.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

==================================================

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