I started from scratch and created all topology files required by MMPBSA
using tleap. Then I re-ran MD with the new topology files. Preliminary
runs of MMPBSA and MMPBSA.MPI based on the new topology files and the
new MD trajectory were successful. Hence, the solution for now was just
skipping the ante-MMPBSA.py step.
Jan-Philip
On 10/07/2011 05:53 PM, Jason Swails wrote:
> 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
>
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Received on Tue Oct 11 2011 - 02:30:03 PDT
