Ok, I'm now getting a really weird problem that has got me scratching my
head. If I take the decomposition parameters out of the mmpbsa.in file, the
script fails with the following error:
----------------------------------------
File "/apps/applications/amber/12/1/default/amber12/bin.real/MMPBSA.py",
line 565, in ?
external_progs, '_MMPBSA_', normal_system)
File
"/apps1/applications/amber/12/1/default/amber12/bin/MMPBSA_mods/calculation.py",
line 176, in run_calculations
calc.Run()
File
"/apps1/applications/amber/12/1/default/amber12/bin/MMPBSA_mods/calculation.py",
line 664, in Run
raise CalcError('%s failed with prmtop %s!\n\t' % (self.program,
CalcError:
/apps/applications/amber/12/1/default/amber12/bin/mmpbsa_py_energy failed
with prmtop
../../../../ALA_Complex_mmpbsa_leap/ProtLigOnly_mmpbsa_ALA_Bound_mbondi.parm!
Exiting. All files have been retained.
----------------------------------------
The _MMPBSA_complex_pb.mdout.0 file has the following info:
----------------------------------------
Reading parm file
(../../../../ALA_Complex_mmpbsa_leap/ProtLigOnly_mmpbsa_ALA_Bound_mbondi.parm)
title:
default_name
Parameter topology includes 10-12 terms:
These are assumed to be zero here (e.g. from TIP3P water)
mm_options: e_debug=3
mm_options: ipb=2
mm_options: inp=2
mm_options: epsin=1.000000
mm_options: epsout=80.000000
mm_options: smoothopt=1
mm_options: istrng=150.000000
mm_options: radiopt=1
mm_options: dprob=1.400000
mm_options: iprob=2.000000
mm_options: npbopt=0
mm_options: solvopt=1
mm_options: accept=0.001000
mm_options: maxitn=1000
mm_options: fillratio=4.000000
mm_options: space=0.500000
mm_options: nfocus=2
mm_options: fscale=8
mm_options: bcopt=5
mm_options: eneopt=2
mm_options: cutnb=0.000000
mm_options: sprob=0.557000
mm_options: cavity_surften=0.005420
mm_options: cavity_offset=0.920000
Processing NetCDF trajectory (_MMPBSA_complex.nc.0)
Processing frame 1
iter Total bad vdW elect nonpolar EPB
frms
----------------------------------
The mmpbsa.in file is as follows:
-----------------------------------------------------
#Sample input file for GB and PB calculation
&general
startframe=1, endframe=4000, interval=2000,
verbose=2, keep_files=0, debug_printlevel=3,netcdf=1,
/
&pb
istrng=0.15, fillratio=4.0,
cavity_offset=0.92, cavity_surften=0.00542,
exdi=80.0, indi=1.0,
radiopt=1,
/
#&decomp
#idecomp=2, dec_verbose=3,
#print_res="1-157, 158",
#/
--------------------------------------------------------
The command used to call the script is:
MMPBSA.py -O -i ../mmpbsa.in -o 01_ALA_01_net_01.out -cp
../../../../ALA_01_mmpbsa_leap/ProtLigOnly_mmpbsa_ALA_Bound_mbondi.parm -y
../../../../01_ALA_01_Traj/md_01.net 1> output.txt 2> error.txt
The error can't be due to the topology file, as when the decomposition
parameters are uncommented and the -do -deo switches put back in, it works
fine. Guess there must be some kind of basic formatting error? If anyone
could point this out, I would be grateful, as I've tried many permutations
with no luck.
On Thu, Aug 1, 2013 at 3:53 PM, George Green <soyo.green.gmail.com> wrote:
> Thanks again for the information. I will run mmpbsa without decomposition
> and use GBSA for decomposition.
>
>
> On Wed, Jul 31, 2013 at 12:21 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>> On Wed, Jul 31, 2013 at 4:08 AM, George Green <soyo.green.gmail.com>
>> wrote:
>>
>> > Thanks for the information. I was unaware that the non polar
>> contribution
>> > could not be decomposed on a per-residue basis.
>> >
>> > However, how is it calculated normally from a stability calculation?
>> There
>> > is no ECAVITY or SASA term in the main outfile (i.e the bit that is not
>> > decomposed). I only get the following output:
>> >
>>
>> I believe you'll have to re-run without decomposition to get the non-polar
>> solvation free energies.
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Thu Aug 01 2013 - 14:00:02 PDT
