AMBER Archive (2007)

Subject: AMBER: implicit minimization

From: Dr. Devanathan Raghunathan (devanathanr_at_bii.a-star.edu.sg)
Date: Thu Sep 27 2007 - 21:21:14 CDT

Hi all,
I have a problem using sander amber9. When I am simulating explicit
solvent systems, it works, but if I try to change the parameter to
implicit solvents (just changed 1 parameter), the calculation is crashed
with the following error :

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
./min.s
------------------------------------------------------------

Exited with exit code 134.

Resource usage summary:

    CPU time : 0.04 sec.
    Max Memory : 2 MB
    Max Swap : 11 MB

    Max Processes : 1
    Max Threads : 1

The output (if any) follows:

[0] MPI Abort by user Aborting program !
prun: /usr/lib/rms/bin/pfloader (host raptor2 process 0 pid 27451)
killed by signal 6 (ABRT)
prun: generating backtrace for /usr/lib/rms/bin/pfloader core.27451
Using host libthread_db library "/lib64/tls/libthread_db.so.1".

warning: core file may not match specified executable file.
Core was generated by `sander -O -i min.in -o min.out -p IVO.prmtop -c
IVO.inpcrd -r min.rst -ref IVO.'.
Program terminated with signal 6, Aborted.
#0 0x0000003e8022e37d in ?? ()
#0 0x0000003e8022e37d in ?? ()
#1 0x0000003e8022faae in ?? ()
#2 0x0000000000000020 in ?? ()
#3 0x0000000000000000 in ?? ()
prun: dumping elan exception state for /usr/lib/rms/bin/pfloader
core.27451

This is my minimization file

Minimization with Cartesian restraints
 &cntrl
   imin=1, maxcyc=200,
   cut=300, igb=7, saltcon=0.2, gbsa=1,
   intdiel=1.0, extdiel=78.5,
   ntpr=10, ntx=1, ntb=0,
   ntr=1
 /

Just changing the igb=7 to igb=0 and removing ntb=0 from the input file
min.in allows the calculation to proceed.
thanks for your insights...
cheers
devan 

-- 
Dr. Devanathan Raghunathan <devanathanr_at_bii.a-star.edu.sg>
Bioinformatics Institute, Agency for Science, Technology and Research

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