Aha. I've found several issues here. I'll start with the topology files.
ante-MMPBSA.py failed you here. It was only designed to work for
protein-ligand systems, (I bash it a little bit in a previous post
yesterday). The reason it didn't work is because it makes the (poor)
assumption that charged termini are only the first and last (non-water/ion)
residues. Thus, there are missing atoms in templates (OXT, for instance)
that causes your topology files to be completely wrong. In fact, tleap
wouldn't even print a prmtop here (but I had to use sleap because there's
something weird about the OFF files created by amberParm that causes tleap
to segfault, if memory serves).
There's a better approach I recently implemented in a separate topology file
editing program that will remove atoms without having to go through leap
(it'll just discard the parameters that no longer apply to your new
molecule). This will be used to create MMPBSA-compatible topologies from
now on. This is why you're getting issues determining LJ parameters.
I included comments on my second error message below:
On Fri, Oct 7, 2011 at 5:45 AM, Jan-Philip Gehrcke
<jgehrcke.googlemail.com>wrote:
> I have exchanged ligand/receptor (starting with ante-MMPBSA), which did
> not improve things. This is the command and the output (notice that I
> did not run the MPI version for now):
>
> $ MMPBSA -i mmpbsa_decomp.in -cp complex_unsolvated.prmtop -sp
> ../topology.top -rp receptor.prmtop -lp ligand.prmtop -use-mdins -y
> ../md_equilibrate_00*
>
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> Warning: Problem parsing L-J 6-12 parameters.
> ptraj found! Using /home/bioinfp/jang/apps/amber11/bin/ptraj
> sander found! Using /apps11/bioinfp/amber10+/bin/sander for GB calculations
> Preparing trajectories for simulation...
> 20 frames were read in and processed by ptraj for use in calculation.
>
> Beginning GB calculations with sander...
> calculating complex contribution...
> calculating receptor contribution...
> bad atom type:
>
This is concerning. This is caught during the setup of radii for the SASA
calculation for GBSA=2 (gbsa==1 assigns the default C parameters to
unrecognized types, but gbsa==2 dies fatally). This is found in
$AMBERHOME/src/sander/mdread.f, IIRC). However, the fact that it was *not*
caught in the complex calculation leads me to believe this is an artifact of
bad topologies caused by what I described above (unless you have a
non-standard atom in your system, like some kind of metal).
I will contact you off-list with fixed topologies.
All the best,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Oct 07 2011 - 09:00:02 PDT
