On Mon, Jun 29, 2015 at 10:30 PM, wliu <wliu.itcs.ecnu.edu.cn> wrote:
> 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.
>
​Have a look at the _MMPBSA_complex_gb.mdout.0 file. Is there an error
message printed there?
The error occurred in the GBSA part, not the normal mode part. The
information here isn't enough to guess what actually happened (since the
real error message should be in the temporary output file... hopefully).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Jun 29 2015 - 21:30:03 PDT
