[AMBER] MMPBSA errors £ºsetting grid spacing larger than solvent probe

From: Fengxue Li <lifx916.126.com>
Date: Mon, 9 Dec 2013 21:25:09 +0800 (CST)

 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
   endframe=50000, verbose=1,
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 Warning 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!
Can anyone help me to calculate freeenergy for this system£¿
Thank you in advance for your help
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Received on Mon Dec 09 2013 - 05:30:02 PST
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