rism.snglpnt (which is all that MMPBSA.py knows how to use for 3D-RISM
calculations) is written in NAB and therefore cannot make use of chamber
topologies.
You can always use cpptraj to get rid of the chamber sections, and it might
work (charges and non-1-4 VDW parameters stay the same), but I haven't
thought about it long enough to say with certainty that this approach won't
miss something.
HTH,
Jason
On Thu, Oct 22, 2015 at 3:33 PM, Josep Maria Campanera Alsina <
campaxic.gmail.com> wrote:
> Dear all,
> I get the following error when trying to decompose (polardecomp=1) the
> solvation free energy from 3D-RISM in MMPBSA.py. The calculation actually
> does a couple of frames and finally crashes.
>
>
> ----------------------------------------------------------------------------------------
> Beginning 3D-RISM calculations with
> /Users/campa/Amber/amber14/bin/rism3d.snglpnt
> calculating complex contribution...
> File "/Users/campa/Amber/amber14/bin/MMPBSA.py.MPI", line 96, in <module>
> app.run_mmpbsa()
> File "/Users/campa/Amber/amber14/bin/MMPBSA_mods/main.py", line 218, in
> run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File "/Users/campa/Amber/amber14/bin/MMPBSA_mods/calculation.py", line
> 79, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File "/Users/campa/Amber/amber14/bin/MMPBSA_mods/calculation.py", line
> 269, in run
> Calculation.run(self, rank, stdout=self.output % rank)
> File "/Users/campa/Amber/amber14/bin/MMPBSA_mods/calculation.py", line
> 148, in run
> self.prmtop))
> CalcError: /Users/campa/Amber/amber14/bin/rism3d.snglpnt failed with prmtop
> AB40.WT-WT.nowat.ildn.pdb.charmm.pdb.psfgen.pdb.amber.top!
> Error occured on rank 0.
> Exiting. All files have been retained.
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>
> ----------------------------------------------------------------------------------------
>
> with the simple following input:
>
> ------------------------------------------
> &general
> startframe=1,endframe=5000,interval=500,verbose=2, keep_files=2, netcdf=1,
> full_traj=1, use_sander=0,
> /
> &rism
> thermo="gf",polardecomp=1,rism_verbose=2,
> /
> ------------------------------------------
>
> The error appears either in serial or parallel calculations in MMPBSA.py
> script of AMBER14. I use the ff99SB-ILDN forcefield and the topology file
> was created originally with chamber but finally converted to "nornal" amber
> topology file with cpptraj facility with the option "parmwrite out ...
> nochamber". The same calculation without the option "polardecomp=1" ends
> correctly. As it seems a problem related with settings of radii (CalcError)
> I've tried to change the radii using parmed but the problem persists.
>
> All comments welcome and thank you very much for the help,
>
> Campa,
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Oct 22 2015 - 13:30:03 PDT
