[AMBER] Normal mode calculation was failed with MMPBSA.py

From: wliu <wliu.itcs.ecnu.edu.cn>
Date: Tue, 30 Jun 2015 10:30:00 +0800

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
   startframe=1000, endframe=1001, interval=1,
   verbose =2,
   entropy =1,
   igb=5, saltcon=0.100
   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 ?
   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
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

I would very much appreciate the helps!


Wei Liu

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Received on Mon Jun 29 2015 - 20:00:02 PDT
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