Hi dear all
I'm trying to calculate free energy with mmpbsa.py in a complex and the
same complex in presence of ions.
I have calculated the free energy for the complex without problems, but
when i try to calculate the free energy for the complex in prescence of
ions I get the next error:
$AMBERHOME/bin/MMPBSA.py -O -i mmpbsa_1b.in -o
RESULTADOS_FINALES_MMPBSA.dat -sp 3LU-COMPLEJO-WAT.prmtop -cp com.prmtop
-rp rec.prmtop -lp lig.prmtop -y 3LU*.mdcrd
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /home/carlos/amber14/bin/mmpbsa_py_energy
cpptraj found! Using /home/carlos/amber14/bin/cpptraj
Preparing trajectories for simulation...
50 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with /home/carlos/amber14/bin/mmpbsa_py_energy
calculating complex contribution...
File "/home/carlos/amber14/bin/MMPBSA.py", line 96, in <module>
app.run_mmpbsa()
File "/home/carlos/amber14/bin/MMPBSA_mods/main.py", line 218, in
run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/home/carlos/amber14/bin/MMPBSA_mods/calculation.py", line 79, in
run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/home/carlos/amber14/bin/MMPBSA_mods/calculation.py", line 148, in
run
self.prmtop))
CalcError: /home/carlos/amber14/bin/mmpbsa_py_energy failed with prmtop
com.prmtop!
Exiting. All files have been retained.
I checked prmtop files with parmed.py and they seem ok. I tried to create
new prmtop files with ante-MMPBSA.py without results.
At the start I followed the next procedure:
tleap:
com = loadpdb 3lu.pdb
rec= loadpdb 3lu-rec-pdb
lig = loadpdb 3lu-lig.pdb
charge com charge = 2.00
charge rec charge = -1.00
charge lig charge = 3.00
saveamberparm rec rec.prmtop rec.inpcrd
saveamberparm lig lig.prmtop lig.inpcrd
addions com Cl- 0
addions com MG 26
saveamberparm com com.prmtop com.inpcrd
solvatebox com TIP3PBOX 8.0
saveamberparm com 3LU-COMPLEJO-WAT.prmtop
quit
I looked the number of atoms in rec.prmtop + lig.prmtop = 5176 and the
number of atoms in com.prmtop is 5204. Then I created a new com.prmtop
called com2.prmtop without Cl- and MG ions but the problem continue.
I will apreciate any sugestion. Thanks in advance
Regards
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Received on Tue Mar 01 2016 - 11:30:03 PST
