Dear All,
I ran a tleap for the protein and combined with the ligand using the script
named "tleap.all" in AMBER12. The script of tleap as follows
source leaprc.ff99SB
source leaprc.gaff
LIG = loadmol2 LIG.mol2
loadamberparams LIG.frcmod
check LIG
receptor = loadPDB rec.pdb
complex = combine {receptor LIG}
set default PBRadii mbondi2
saveAmberParm LIG LIG.top LIG.crd
saveAmberParm receptor rec.top rec.crd
saveAmberParm complex com.top com.crd
savepdb complex complex_gas.pdb
charge complex
addIons2 complex Cl- 0
solvateBox complex TIP3PBOX 10.0
saveAmberParm complex com_solvated.top com_solvated.crd
savepdb complex com_solvated.pdb
quit
The log file of tleap is enclosed in attachment. Further I ran md in
AMBER14 and was successful for 5ns. Further I ran MMPBSA using the script
named "mmpbsa.in and mmpbsa_SUB" (enclosed in attachment) in AMBER14 and I
got the following error for "com.top" (enclosed in attachment) which was
generated while running the script "tleap.all". Can you please guide me to
solve this problem in calculating binding free energies?
Error:
ligand comples using the
bad atom type: br
File "/cbio/jclab/projects/collab/amber14/bin/MMPBSA.py.MPI", line 96, in
<module>
app.run_mmpbsa()
File "/cbio/jclab/projects/collab/amber14/bin/MMPBSA_mods/main.py", line
218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/cbio/jclab/projects/collab/amber14/bin/MMPBSA_mods/calculation.py", line
79, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/cbio/jclab/projects/collab/amber14/bin/MMPBSA_mods/calculation.py", line
148, in run
self.prmtop))
CalcError: /cbio/jclab/projects/collab/amber14/bin/sander failed with
prmtop com.top!
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
Thanks & regards
*Ramesh M*
Email: shreeramesh.gmail.com
Mobile: (91) + 9646469938 (27) + (0) 844556164
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Received on Thu Apr 02 2015 - 00:30:02 PDT
