Hi, all
I have a problem with MMPBSA.py for normal mode calculation. My
input file was written as:
Input file for running PB and GB
&general
startframe=1000, endframe=1001, interval=1,
verbose =2,
entropy =1,
strip_mask=:WAT:Cl-
/
&gb
igb=5, saltcon=0.100
/
&nmode
nmstartframe=1, nmendframe=1, nminterval=1,
maxcyc=40000, drms=0.0001
/
Then I get the error information as follow:
/run_2014_6_27.sh: line 2: 25045 Terminated MMPBSA.py -O -i
mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -use-mdins -sp cmp.prmtop -cp
com_nobox.prmtop -rp pro.prmtop -lp lig.prmtop -y
../sbf-1_mmpbsa_py/*.crd > progress.log
File "/apps/amber14//bin/MMPBSA.py", line 104, in ?
app.run_mmpbsa()
File "/apps/amber14/bin/MMPBSA_mods/main.py", line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/apps/amber14/bin/MMPBSA_mods/calculation.py", line 79, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/apps/amber14/bin/MMPBSA_mods/calculation.py", line 147, in run
raise CalcError('%s failed with prmtop %s!' % (self.program,
CalcError: /apps/amber14/bin/mmpbsa_py_energy failed with prmtop
com_nobox.prmtop!
Exiting. All files have been retained.
I used ff14SB force field for four prmtop files (protein, ligand,
protein-ligand, protein-ligand-water-ion). Why did this protein-ligand
prmtop file failed? My tleap script leap.in was written as:
source leaprc.ff14SB
source leaprc.gaff
frcmod03 = loadamberparams frcmod.ionsff99_tip3p
loadamberprep test.prepi
loadamberparams test.frcmod
pro = loadpdb 1uu7_nmr.pdb
lig = loadpdb ligand.pdb
com = combine {pro lig}
set default PBRadii mbondi2
saveamberparm pro pro.prmtop pro.inpcrd
saveamberparm lig lig.prmtop lig.inpcrd
saveamberparm com com_nobox.prmtop com_nobox.inpcrd
charge com
solvateoct com TIP3PBOX 12.0
addions com Cl- 0
savepdb com complex.pdb
saveamberparm com cmp.prmtop cmp.inpcrd
quit
I would very much appreciate the helps!
Regards,
Wei Liu
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Received on Mon Jun 29 2015 - 20:00:02 PDT
