AMBER Archive (2009)

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

From: 欧阳德方 (ouyangdf1978_at_hotmail.com)
Date: Mon Dec 07 2009 - 16:30:41 CST

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_at_uci.edu
> To: amber_at_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_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
> >
> >
> > _________________________________________________________________
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> >
> >
>
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