[gmx-users] Issue in ligand gyration analysis
Sainitin Donakonda
saigro16 at gmail.com
Fri Aug 23 15:38:22 CEST 2013
Thank justin for reply i also thought same i used gromacs 4.5.5 here so
just now i used gromacs 4.5.4 it works perfectly but choosing ligand only
gives value as zero..can you tell me what might be the reason ?
Thanks,
Nitin
On Fri, Aug 23, 2013 at 3:12 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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 <http://libdl-2.15.so>
>> 7fdbb8895000-7fdbb8a95000 ---p 00002000 08:02 2354860
>> /lib/x86_64-linux-gnu/libdl-2.**15.so <http://libdl-2.15.so>
>> 7fdbb8a95000-7fdbb8a96000 r--p 00002000 08:02 2354860
>> /lib/x86_64-linux-gnu/libdl-2.**15.so <http://libdl-2.15.so>
>> 7fdbb8a96000-7fdbb8a97000 rw-p 00003000 08:02 2354860
>> /lib/x86_64-linux-gnu/libdl-2.**15.so <http://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 <http://libm-2.15.so>
>> 7fdbb925e000-7fdbb945d000 ---p 000fb000 08:02 2355059
>> /lib/x86_64-linux-gnu/libm-2.**15.so <http://libm-2.15.so>
>> 7fdbb945d000-7fdbb945e000 r--p 000fa000 08:02 2355059
>> /lib/x86_64-linux-gnu/libm-2.**15.so <http://libm-2.15.so>
>> 7fdbb945e000-7fdbb945f000 rw-p 000fb000 08:02 2355059
>> /lib/x86_64-linux-gnu/libm-2.**15.so <http://libm-2.15.so>
>> 7fdbb945f000-7fdbb9477000 r-xp 00000000 08:02 2354979
>> /lib/x86_64-linux-gnu/libpthre**ad-2.15.so <http://libpthread-2.15.so>
>> 7fdbb9477000-7fdbb9676000 ---p 00018000 08:02 2354979
>> /lib/x86_64-linux-gnu/libpthre**ad-2.15.so <http://libpthread-2.15.so>
>> 7fdbb9676000-7fdbb9677000 r--p 00017000 08:02 2354979
>> /lib/x86_64-linux-gnu/libpthre**ad-2.15.so <http://libpthread-2.15.so>
>> 7fdbb9677000-7fdbb9678000 rw-p 00018000 08:02 2354979
>> /lib/x86_64-linux-gnu/libpthre**ad-2.15.so <http://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 <http://libc-2.15.so>
>> 7fdbb9fbb000-7fdbba1ba000 ---p 001b5000 08:02 2354975
>> /lib/x86_64-linux-gnu/libc-2.**15.so <http://libc-2.15.so>
>> 7fdbba1ba000-7fdbba1be000 r--p 001b4000 08:02 2354975
>> /lib/x86_64-linux-gnu/libc-2.**15.so <http://libc-2.15.so>
>> 7fdbba1be000-7fdbba1c0000 rw-p 001b8000 08:02 2354975
>> /lib/x86_64-linux-gnu/libc-2.**15.so <http://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 <http://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 <http://ld-2.15.so>
>> 7fdbba77a000-7fdbba77c000 rw-p 00023000 08:02 2355066
>> /lib/x86_64-linux-gnu/ld-2.15.**so <http://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 <jalemkul at outerbanks.umaryland.edu> | (410)
> 706-7441
>
> ==============================**====================
> --
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