I have been trying to use mmpbsa.py- the MPI version- to analyze the binding energy derived from a trajectory obtained using pmemd. I keep getting the following error:
Calculations complete. Writing output file(s)...
Error: Sander output is missing values!
VDWAALS = ************* EEL = -23028.8786 EGB = -4065.0313
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py --clean to erase these files.
MPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize()
MPI: aborting job
It does indeed go on to write the final .dat file with the results in it, however, none of the binding energy values are written- only that it has recognized the proper ligand and recpetor masks.
I have seen this problem when searching this forum, but have not yet seen a solution for me.
I have generated the topoly files using the following script-run as tleap -f script
here is the script:
source leaprc.ff99SB
source leaprc.gaff
loadAmberParams CTZ_mod1_112812_prodrg.frcmod
CTZ = loadMol2 CTZ_mod1_112812_prodrg.mol2
saveoff CTZ ctz.lib
receptor = loadPDB 2psj_112812_nowat.pdb
complex = combine {receptor CTZ}
set default PBRadii mbondi2
saveAmberParm CTZ lig.top lig.crd
saveAmberParm receptor rec.top rec.crd
saveAmberParm complex com.top com.crd
loadamberparams frcmod.ionsjc_tip3p
addions complex Na+ 0
solvatebox complex TIP3PBOX 9.0
saveAmberParm complex com_solvated.top com_solvated.crd
quit
I can see no problems in the pmemd runs. I have looked at the trajectory in vmd and all looks well. I have also looked at the .mdout file from the production run-again there are no problems.
However, when I look at the complex in VMD- all the bonds seem distorted like I didn't use the periodic box option in loading the file. I have tried loading aa few forms of the topology file. Nothing seems to work.
I just can't seem to find what's wrong here and think it has something to do with pmemd and mmpbsa.py MPI
Can anyone point me in the right direction?
Chris
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Received on Fri Feb 08 2013 - 16:30:02 PST
