AMBER Archive (2009)

Subject: Re: [AMBER] Problem of MM-PBSA

From: Ray Luo (ray.luo_at_uci.edu)
Date: Mon Dec 07 2009 - 12:19:02 CST

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_at_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
>
>
> _________________________________________________________________
> 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
>
>

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber