[AMBER] MMPBSA.py.MPI and matching topology files a problem

From: Kasprzak, Wojciech (NIH/NCI) [C] <"Kasprzak,>
Date: Tue, 8 May 2018 16:17:21 +0000

Dear Amber Users,

I am trying to run MMPBSA.py.MPI (Amber 16) protocol using three input trajectories:
1. complex (RNA + ligand ) in solvent
2. receptor (RNA) in solvent
3 ligand in solvent

The runs were set-up independently (separate LEaP sessions) but are consistent with each other.
The protocol works fine as long as I keep the original systems intact (full size).

What I want to do is to run it on a subset of the target atoms near the ligand and the ligand itself.

To that effect I ran ante-MMPBSA.py with the COMPLEX-SOLVENT-ORIGINAL.prmtop file as input and created:
1. COMPLEX-NOSOLV-ANTE.prmtop - stripped of water, ions, and the selected RNA atoms outside the area of
                                                             RNA-ligand interface
2. RECEPTOR-NOSOLV-ANTE.prmtop - RNA fragment matching what's left in the above
3. LIGAND-NOSOLV-ANTE.prmtop - full ligand from the PRMTOP in 1.

The numbers of atoms and the atoms listed appear to be correct.

Then, I tried to run MMPBSA.py.MPI with the following six topology files:
-sp COMPLEX-SOLVENT-ORIGINAL.prmtop - full size complex in solvent
-cp COMPLEX-NOSOLV-ANTE.prmtop - stripped complex (with receptor fragment)

-srp RECEPTOR-SOLVENT-ORIGINAL.prmtop - full size receptor in solvent
-rp RECEPTOR-NOSOLV-ANTE.prmtop - stripped receptor fragment

-slp LIGAND-SOLVENT-ORIGINAL.prmtop - ligand in full solvent
-lp LIGAND-NOSOLV-ANTE.prmtop - stripped full ligand

... and the three original trajectories (full solvent runs) as input:
-y FULL-COMPLEX-IN-SOLVENT.nc - with strip_mask in mmpbsa.in as in ante-MMPBSA.py

The mmpbas.in contains the following general parameter definitions:
  endframe=10000, verbose=1, netcdf=1, strip_mask=":1-10,22-46,52-61,63-69225"

The computation starts running, but crashes with a "CalcError: cpptraj failed with prmtop RECEPTOR-NOSOLV-ANTE.prmtop"
Without the strip_mask, the error is "CalcError: mmpbsa_py_energy failed with prmtop RECEPTOR-NOSOLV-ANTE.prmtop"
Attempts to add receptor_mask definition to mmpbsa.in are ignored: "UserWarning: receptor_mask overwritten with default"

I cannot guess what else I could try. The errors always point to RECEPTOR-NOSOLV-ANTE.prmtop as the problem, and the
inability to read the trajectory with a receptor mask alarms me, but I don't know how to deal with it.
Should I cpptraj the receptor trajectory and strip it down to the target atoms' subset before using it as input to MMPBSA?
Any hints or comments would be much welcome.

Thnak you in advance, Voytel

Wojciech (Voytek) Kasprzak (Contractor)
Analyst Programmer
Frederick National Laboratory for Cancer Research
Leidos Biomedical Research, Inc.
Post Office Box B
Frederick, Maryland 21702
Phone: 301-846-5537

AMBER mailing list
Received on Tue May 08 2018 - 09:30:03 PDT
Custom Search