Dear amber users, Recently, i am trying to compare the binding free energy of a ligand with its different mutant receptors by the MM/PBSA module in AMBER10.The first step passed without a hitch and i got 200 sets of coordinates.However, when i tried to calculate the binding energy with the perl script,i couldn't get the statistics.out file as before. I checked the log file and found the warning information that i listed below. I searched the archive of our mailing list where someone has proposed this problem several years ago, but there may still don't have a valid solution for this problem. Any suggestions are greatly appreciated! Thanks in advance! Jacob Error information form log file :=>> Doing statistics=>> Values of global variables TEMP = 300 R = 8.314 gammaP = 0.0072 betaP = 0.00 gammaG = 0.0072 betaG = 0.00=>> Reading input=>> Reordering files Final
order: 1. snapshot_com.all.out: - 2. snapshot_rec.all.out: - 3. snapshot_lig.all.out: -=>> Reading files Reading snapshot_com.all.out WARNING: Missing PBNONPOL for PB in 0 -> Taken from -1WARNING: Missing ELRAELE for PB in 0 -> Taken from -1 WARNING: Missing EPB for PB in 0 -> Taken from -1 WARNING: Missing VDWNB for MM in 1 -> Taken from 0 WARNING: Missing VDW14 for MM in 1 -> Taken from 0 WARNING: Missing PBNONPOL for PB in 1 -> Taken from 0 WARNING: Missing ELRAELE for PB in 1 -> Taken from 0 WARNING: Missing PBCAV for PB in 1 -> Taken from 0 WARNING: Missing EPB for PB in 1 -> Taken from 0 WARNING: Missing SURF for MS in 1 -> Taken from 0 ...........=>> Treat special parameters=>> Calc missing parameters Processing MM GAS Doing 1 MM ELE No values for MM_ELE existing -> Skipping
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Received on Thu Mar 03 2011 - 08:30:10 PST
