Hi,all
When I
used the MM-PBSA method as implemented in AMBER 11 to calculate the binding free energy,I
created a solvent box including A and B solvent¡£this is my file £º mmpbsa.in
Input file for running PB
&general
endframe=50000, verbose=1,
/
&pb
istrng=0.15, fillratio=4, scale=0.5, exdi=19.0
/
MMPBSA -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp comp_mix.prmtop -cp comp.prmtop -rp host.prmtop -lp dea.prmtop -y md1.mdcrd
to calculate free energy£¬this error is
calculating receptor contribution...
PB Waring in pb_read(): setting grid spacing larger than solvent probe
may cause numerical instability if ipb=1
PB Info in pb_read(): npopt has been overwritten with inp
Total surface charge 0.0045
Reaction field energy -149.3438
Cavity solvation energy 11.1404
Total surface charge 0.1397
Reaction field energy -1523.3429
Cavity solvation energy 72.9324
Total surface charge 0.1413
Reaction field energy -1876.4292
Cavity solvation energy 65.1309
SA Bomb in circle(): Stored surface points over limit 594240
Error: mmpbsa_py_energy error during PB calculations!
you suggest that i may run with the latest version of AmberTools,Then I
used the MM-PBSA method as implemented in AMBER 12 and AmberTools 13 to calculate the binding free energy,this error is
Beginning PB calculations with /opt/amber12/bin/mmpbsa_py_energy
calculating complex contribution...
CalcError: /opt/amber12/bin/mmpbsa_py_energy failed with prmtop comp.prmtop!
Exiting. All files have been retained
.
Can anyone help me to calculate freeenergy for this system£¿
Thank you in advance for your help
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Received on Tue Dec 10 2013 - 02:00:02 PST
