From: konda003 . <konda003.gmail.com>
Date: Thu, 16 Feb 2017 15:02:35 -0500


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.
 startframe=9901, endframe=10000, interval=20, verbose=2, keep_files=2,
  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

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>
  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__
  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
 startframe=9901, endframe=10000, interval=20, verbose=2, keep_files=2,
  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,

AMBER mailing list

Received on Thu Feb 16 2017 - 12:30:03 PST
Custom Search