Dear Experts,
I am trying to use mm_pbsa.pl to calculate binding free energy between a protein and RNA.The length of trajectory is 30ns. I selected about 31 snapshots from the beginning to the end. The program always stopped in the middle of the procedure and the outfile 'binding_energy.log' gave the errors:
Calc contrib for ./snapshot_com.crd.7
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
/home/programs/amber/amber14/bin/sander -O -i pbsa_com.in -o pbsa_com.7.out -c ./snapshot_com.crd.7 -p ./com.prmtop not successful
For details see: http://ambermd.org/Questions/mm_pbsa.html#pbsa_command_not_successful
I followed the indications to search for '
http://ambermd.org/Questions/mm_pbsa.html#pbsa_command_not_successful'.I did not find the error mentioned in the webpage in my 'pbsa_com.7.out' but errors as following:
NSTEP ENERGY RMS GMAX NAME NUMBER
1 NaN NaN 1.3733E+07 O 8437
BOND = ************* ANGLE = 1406040.6688 DIHED = 44721.8728
VDWAALS = NaN EEL = +Infinity EPB = -56004.1098
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
ECAVITY = 311026.9588 EDISPER = 0.0000
Could you please suggest me how to solve this problem?
Thanks in advance.
yhz
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Received on Thu Apr 14 2016 - 01:00:04 PDT
