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 Sun Dec 06 2009 - 21:30:02 PST
