Dear Ouyang,
Since it stopped right at the GB/MM/SAS step, it doesn't matter whether
you use PB or GB, it is the sander that gives you the problem.
So can you reproduce the problem by running sander by hand? If yes, you
probably need to check whether the ligand files are self consistent ...
for example by visualizing them in VMD ...
In general, it is much helpful if you know the flow of the script, i.e.
what is done at each step, for you to spot any problem.
All the best,
Ray
==========================================
Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email: rluo.uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================
欧阳德方 wrote:
> Hi, Ray,
>
> I have pass all test cases after the Amber installation and did some mm-pbsa jobs before and it works well. This time the problem is mainly that mm-pbsa stops when run snapshot_lig.crd.1. The receptor and complex are fine.
>
> Regards,
> Ouyang
>
>
>> Date: Mon, 7 Dec 2009 10:19:02 -0800
>> From: ray.luo.uci.edu
>> To: amber.ambermd.org
>> Subject: Re: [AMBER] Problem of MM-PBSA
>>
>> Dear Ouyang,
>>
>> Can pass all test cases after the Amber installation? Note that the
>> mmpbsa test cases are inside $AMBERHOME/src/mmpbsa. Make sure all mmpbsa
>> test cases can pass before running your own jobs.
>>
>> All the best,
>> Ray
>>
>> ==========================================
>> Ray Luo, Ph.D.
>> Associate Professor
>> Dept Molecular Biology & Biochemistry
>> University of California, Irvine, CA 92697
>> USPS: PO Box 3900 Email: rluo.uci.edu
>> Phones: (949) 824-9528, 9562
>> Web: http://rayl0.bio.uci.edu/
>> ==========================================
>>
>>
>>
>> 欧阳德方 wrote:
>>
>>> Dear all,
>>>
>>> When I run MM-PBSA to calculate the binding energy of ligand-receptor complex. When I run the command: mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log.
>>> Atom number of receptor: 1335; atom number of ligand: 528; atom number of the complex (including water and counterions): 32769.
>>> All the parameters are the same as AMBER tutorial "MM-PBSA".
>>>
>>> There is a problem as follows:
>>> *** glibc detected *** /usr/local/amber9/exe/sander: double free or corruption (out): 0x0000000001f4c8e0 ***
>>> ======= Backtrace: =========
>>> /lib64/libc.so.6[0x35d9a72832]
>>> /lib64/libc.so.6(cfree+0x8c)[0x35d9a75f2c]
>>> /usr/local/amber9/exe/sander[0x4ae56e]
>>> /usr/local/amber9/exe/sander[0x47da52]
>>> /usr/local/amber9/exe/sander[0x47c32c]
>>> /usr/local/amber9/exe/sander[0x863bce]
>>> /lib64/libc.so.6(__libc_start_main+0xf4)[0x35d9a1e074]
>>> /usr/local/amber9/exe/sander[0x401b09]
>>> ======= Memory map: ========
>>> 00110000-001a6000 r-xp 00000000 08:01 4482863 /usr/lib64/libgfortran.so.1.0.0
>>> 001a6000-003a5000 ---p 00096000 08:01 4482863 /usr/lib64/libgfortran.so.1.0.0
>>> 003a5000-003a7000 rw-p 00095000 08:01 4482863 /usr/lib64/libgfortran.so.1.0.0
>>> 00400000-008b0000 r-xp 00000000 08:01 562545 /usr/local/amber9/exe/sander
>>> 00ab0000-00ac7000 rw-p 004b0000 08:01 562545 /usr/local/amber9/exe/sander
>>> 00ac7000-017d0000 rw-p 00ac7000 00:00 0
>>> 01f46000-01f67000 rw-p 01f46000 00:00 0 [heap]
>>> 35d8800000-35d881b000 r-xp 00000000 08:01 2056372 /lib64/ld-2.7.so
>>> 35d8a1a000-35d8a1b000 r--p 0001a000 08:01 2056372 /lib64/ld-2.7.so
>>> 35d8a1b000-35d8a1c000 rw-p 0001b000 08:01 2056372 /lib64/ld-2.7.so
>>> 35d9a00000-35d9b4d000 r-xp 00000000 08:01 2056374 /lib64/libc-2.7.so
>>> 35d9b4d000-35d9d4d000 ---p 0014d000 08:01 2056374 /lib64/libc-2.7.so
>>> 35d9d4d000-35d9d51000 r--p 0014d000 08:01 2056374 /lib64/libc-2.7.so
>>> 35d9d51000-35d9d52000 rw-p 00151000 08:01 2056374 /lib64/libc-2.7.so
>>> 35d9d52000-35d9d57000 rw-p 35d9d52000 00:00 0
>>> 35d9e00000-35d9e82000 r-xp 00000000 08:01 2056376 /lib64/libm-2.7.so
>>> 35d9e82000-35da081000 ---p 00082000 08:01 2056376 /lib64/libm-2.7.so
>>> 35da081000-35da082000 r--p 00081000 08:01 2056376 /lib64/libm-2.7.so
>>> 35da082000-35da083000 rw-p 00082000 08:01 2056376 /lib64/libm-2.7.so
>>> 35e2a00000-35e2a0d000 r-xp 00000000 08:01 2056576 /lib64/libgcc_s-4.1.2-20070925.so.1
>>> 35e2a0d000-35e2c0d000 ---p 0000d000 08:01 2056576 /lib64/libgcc_s-4.1.2-20070925.so.1
>>> 35e2c0d000-35e2c0e000 rw-p 0000d000 08:01 2056576 /lib64/libgcc_s-4.1.2-20070925.so.1
>>> 7fb87c000000-7fb87c021000 rw-p 7fb87c000000 00:00 0
>>> 7fb87c021000-7fb880000000 ---p 7fb87c021000 00:00 0
>>> 7fb882abe000-7fb882b30000 rw-p 7fb882abe000 00:00 0
>>> 7fb882b51000-7fb882b53000 rw-p 7fb882b51000 00:00 0
>>> 7fff8ab3d000-7fff8ab52000 rw-p 7ffffffea000 00:00 0 [stack]
>>> 7fff8abfe000-7fff8abff000 r-xp 7fff8abfe000 00:00 0 [vdso]
>>> ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
>>> /usr/local/amber9/exe/sander -O -i sander_lig.in -o sander_lig.1.out -c ./snapshot_lig.crd.1 -p ./4+G0_6.prmtop not successful
>>>
>>> The binding_energy.log is as follows:
>>> "=>> Init data
>>> Presuming executables of amber suite to be in /usr/local/amber9/exe
>>>
>>> =>> Reading input parameters
>>> Found PREFIX => snapshot
>>> Found PATH => ./
>>> Found COMPLEX => 1
>>> Found RECEPTOR => 1
>>> Found LIGAND => 1
>>> Found COMPT => ./4+G0_new0.6_vac.prmtop
>>> Found RECPT => ./rna_vac.prmtop
>>> Found LIGPT => ./4+G0_6.prmtop
>>> Found GC => 0
>>> Found AS => 0
>>> Found DC => 0
>>> Found MM => 1
>>> Found GB => 1
>>> Found PB => 0
>>> Found MS => 1
>>> Found NM => 0
>>> Found PROC => 2
>>> Found REFE => 0
>>> Found INDI => 1.0
>>> Found EXDI => 80.0
>>> Found SCALE => 2
>>> Found LINIT => 1000
>>> Found PRBRAD => 1.4
>>> Found ISTRNG => 0.0
>>> Found RADIOPT => 0
>>> Found NPOPT => 1
>>> Found CAVITY_SURFTEN => 0.0072
>>> Found CAVITY_OFFSET => 0.00
>>> Found SURFTEN => 0.0072
>>> Found SURFOFF => 0.00
>>> Found DIELC => 1.0
>>> Found IGB => 2
>>> Found GBSA => 1
>>> Found SALTCON => 0.00
>>> Found EXTDIEL => 80.0
>>> Found INTDIEL => 1.0
>>> Found SURFTEN => 0.0072
>>> Found SURFOFF => 0.00
>>> Found PROBE => 0.0
>>>
>>> =>> Checking sanity
>>> Checking GENERAL
>>> Checking MM
>>> Checking GB
>>> Checking MS
>>>
>>> =>> Creating input
>>> Sander input
>>>
>>> =>> Calculating energy / entropy contributions
>>> Calc contrib for ./snapshot_com.crd.1
>>> Calc MM/GB/SAS
>>> Generate PDB
>>> Center PDB
>>> Generate PQR
>>> Calc MS
>>> Calc contrib for ./snapshot_com.crd.2
>>> Calc MM/GB/SAS
>>> Generate PDB
>>> Center PDB
>>> Generate PQR
>>> Calc MS
>>> Calc contrib for ./snapshot_com.crd.3
>>> Calc MM/GB/SAS
>>> Generate PDB
>>> Center PDB
>>> Generate PQR
>>> Calc MS
>>> Calc contrib for ./snapshot_com.crd.4
>>> Calc MM/GB/SAS
>>> Generate PDB
>>> Center PDB
>>> Generate PQR
>>> Calc MS
>>> Calc contrib for ./snapshot_com.crd.5
>>> Calc MM/GB/SAS
>>> Generate PDB
>>> Center PDB
>>> Generate PQR
>>> Calc MS
>>> ----
>>> Calc contrib for ./snapshot_rec.crd.99
>>> Calc MM/GB/SAS
>>> Generate PDB
>>> Center PDB
>>> Generate PQR
>>> Calc MS
>>> Calc contrib for ./snapshot_rec.crd.100
>>> Calc MM/GB/SAS
>>> Generate PDB
>>> Center PDB
>>> Generate PQR
>>> Calc MS
>>> Calc contrib for ./snapshot_lig.crd.1
>>> Calc MM/GB/SAS"
>>> It stoped at snapshot_lig.crd.1.
>>> I try MM-GBSA and get the same problem.
>>> Thanks a lot for your help!
>>>
>>> Merry Christmas!
>>>
>>> Regards,
>>> Ouyang
>>>
>>>
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Received on Mon Dec 07 2009 - 15:00:03 PST
