Hi,
i run mmpbsa calculation with amber10,
i have successfully extracted the coordinates from mdcrd.
but when i run script "binding_energy.mmpbsa" for calculation of its binding
energy.
The calculation stop with following error message:
sander -O -i pbsa_lig.in -o pbsa_lig.89.out -c ./snapshot_lig.crd.89 -p
./raf.prmtp not successful
PB Bomb in setgrd(): focusing grid too large 2
reset fillratio to a larger number 2.000
then I searched for this error and i got result on link "
http://www.teokem.lu.se/~ulf/Methods/mm_pbsa.html"
then added the following line (#435) to $AMBERHOME/src/mm_pbsa/
mm_pbsa_createinput.pm:
print OUT " fillratio=3 \n";
But still the error persist.
What to do please help me.
Thanking you
--
*Prajwal Nandekar
Ph. D. Scholar
Department of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research (NIPER)
Sector 67, S.A.S. Nagar, (Punjab) INDIA-160062
Mob. 09780741228*
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Received on Mon Oct 17 2011 - 23:30:03 PDT
