AMBER Archive (2009)

Subject: [AMBER] Problem of MM-PBSA

From: 欧阳德方 (ouyangdf1978_at_hotmail.com)
Date: Sun Dec 06 2009 - 23:09:47 CST

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

                                               
_________________________________________________________________
MSN十年回馈，每位用户可免费获得价值25元的卡巴斯基反病毒软件2010激活码，快来领取！
http://kaba.msn.com.cn/?k=1
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber