Hi,
I am running MMPBSA for the carbon nanotube (named as C20) and eight drugs
( named as DOA,DOB,DOC,DOD,PTA,PTB,PTC,PTD) complex. The complex pdb is
attached for your information.
Here, I am trying to calculate the binding free energy for the C20 and DOA
from the above complex. Later, I wanna try for C20 and DOB, C20 and DOC and
so on from the above complex.
The MMPBSA input file for the last 5 frames.
&general
startframe=9901, endframe=10000, interval=20, verbose=2, keep_files=2,
strip_mask=:DOB:DOC:DOD:PTA:PTB:PTC:PTD,
/
&pb
istrng=0.100, inp=1,
fillratio=4, radiopt=0,
/
The command used
$AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL.dat -sp
com_solvated.prmtop -cp com.prmtop -rp c20.prmtop -lp doa.prmtop -y
5md.mdcrd
The error for the above job is
Loading and checking parameter files for compatibility...
File "/usr/local/amber16/bin/MMPBSA.py", line 98, in <module>
app.loadcheck_prmtops()
File "/usr/local/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 572, in loadcheck_prmtops
FILES.receptor_prmtop, FILES.ligand_prmtop)
File "/usr/local/amber16/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py",
line 109, in __init__
self._validate()
File "/usr/local/amber16/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py",
line 876, in _validate
raise PrmtopError('Complex natom != receptor natom + ligand natom')
PrmtopError: Complex natom != receptor natom + ligand natom
*I have tried in other way too,*
I have stripped the DOB,DOC,DOD,PTA,PTB,PTC,PTD and WAT molecules from the
above complex and created the stripped_com.prmtop and stripped_com.mdcrd
files with C20 and DOA only.
The mmpbsa input is
&general
startframe=9901, endframe=10000, interval=20, verbose=2, keep_files=2,
/
&pb
istrng=0.100, inp=1,
fillratio=4, radiopt=0,
/
The command used is
$AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL.dat -cp
stripped_com.prmtop -rp c20.prmtop -lp doa.prmtop -y stripped_com.mdcrd
The Job is successully done, but the error is that dihedral energy for the
complex is around 60. I checked the complex, receptor, ligand prmtop and
inpcrd files (generated from MMPBSA.py), there are no strange bonds.
P.S: I have used AMBER 16 and AMBERTOOLS 16. The simulations were performed
using pmemd.CUDA. The PBRadii mbondi2 was set.
Best Regards,
KK
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Received on Thu Feb 16 2017 - 12:30:03 PST
