Bill, thank you for the reply.
The case of mmgbsa calculation is this. The input is a ternary complex which consists of protein(187 residues),peptide(12 residues) and one ligand. The aim is to calculate mmgbsa for this ternary complex. In this case, protein (A) + peptide (B) is treated as receptor while ligand (C) is treated as ligand itself and so simply said, [A+B] + C. Calculations showed reasonable values obtained from both MMPBSA.PL and MMPBSA.PY.
The problem I face now is when I tried to use the same trajectory from [A+B] + C and aim to calculate mmgbsa for [A+C] + B, both modules of MMPBSA.PL and MMPBSA.PY didnt work. Using mmpbsa.pl previously, I got insensible numerical values.Moreover, upon using recently the mmpbsa.py, it wasn't able to recognize the -cp (complex prmtop) input as well as -y (complex mdcrd). Please be reminded that I used the same -cp and -y inputs for both [A+B] + C and [A+C] + B.
Below is the comparison of mmpbsa.py input file. For testing, I used 50 frames from trajectory.
1. The [A+B]+C system
MMPBSA.py input file for running GB
&general
interval=1,
verbose=2, strip_mdcrd=1,
/
&gb
igb=2, surften=0.0072
/
# Execute the program
$DO_PARALLEL $EXE -O -i mmpbsa.in \
-sp ./ABC_solvated.prmtop \
-cp ./ABC.prmtop \
-rp ./AB.prmtop \
-lp ./C.prmtop \
-y ./ABC50f.mdcrd
2>>mmpbsa.out 1>>mmpbsa.out
/home/biiamorasj/2011/awk/dacdif -t 3 -a 0.2
FINAL_RESULTS_MMPBSA.dat.save FINAL_RESULTS_MMPBSA.dat
2. The [A+C]+B system
MMPBSA.py input file for running GB
&general
interval=1,
verbose=2, strip_mdcrd=1,
receptor_mask=':1-3055 3279-3327',
ligand_mask=':3056-3278',
# entropy=1,
/
&gb
igb=2, surften=0.0072
/
# Execute the program
$DO_PARALLEL $EXE -O -i mmpbsa.in \
-sp ./ABC_solvated.prmtop \
-cp ./ABC.prmtop \
-rp ./AC.prmtop \
-lp ./B.prmtop \
-y ./ABC50f.mdcrd 2>>mmpbsa.out 1>>mmpbsa.out
/home/biiamorasj/2011/awk/dacdif -t 3 -a 0.2 FINAL_RESULTS_MMPBSA.dat.save FINAL_RESULTS_MMPBSA.dat
Tracing back where mmpbsa.py script knock-off, the lsf.out shows:
ptraj found! Using /usr/local/amber11/bin/ptraj
sander found! Using /usr/local/amber10_serial/amber10/bin/sander
Assuming /usr/local/amber10_serial/amber10/bin/sander is part of
amber9 or amber10. Using old PB input file.
Error: Specified file (mdcrd) does not exist!
And, mmpbsa.out shows:
./Run.GB: line 37: -cp: command not found
My own interpretation of the error cause:
1. It seems to me that mmpbsa.py dont recognize the -y input mdcrd in [A+C]+B calculation after I implemented different numbering codes for receptor and ligand. What type of -y input does mmpbsa.py requires considering in this case I used two parts receptor.
2.It seems to me that the "-cp: command not found'' error flag does not recognize the 'ABC.prmtop' for [A+C]+B calculation.
Thanks in advance for taking the time to read this post and suggestions as well.
Amor
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Received on Mon Jul 19 2010 - 01:30:05 PDT
