Hi, amber,
When I use MMPBSA/GBSA to do decomposition analysis, I come across errors as follows,
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
ptraj found! Using /home/tianchuan/amber11/bin/ptraj
sander found! Using /home/tianchuan/amber11/bin/sander for GB calculations
sander found! Using /home/tianchuan/amber11/bin/sander for PB calculations
Preparing trajectories for simulation...
600 frames were read in and processed by ptraj for use in calculation.
Beginning GB calculations with sander...
calculating complex contribution...
Unit 16 Error on OPEN: _MMPBSA_.restrt
Error: sander error during GB calculations!
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py --clean to erase these files.
This is my input files
&general
startframe=1562, endframe=13561, interval=20, keep_files=2,
/
&gb
igb=5, saltcon=0.100,
/
&pb
istrng=0.100,
/
&decomp
idecomp=2, print_res="1-466"
dec_verbose=3,
And I use this command to perform MMPBSA
$AMBERHOME/bin/MMPBSA -O -i MMPBSA_decomp.in -o FINAL_MMPBSA.dat -do FINAL_DECOMP_MMPBSA.dat -sp com-ome-R-solvated.prmtop -cp com-ome-R.prmtop -rp protein-ome-R.prmtop -lp OMR.prmtop -y md3.mdcrd >& md1.log
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Received on Mon Aug 05 2013 - 19:00:02 PDT
