PROBLEM SOLVED
Just in case someone else encounters this problem- here was the solution in my case. The complex topology was wrong, and it has something to do with the 'combine' command as given in the example in the mmpbsa.py manual
here is my script:
source leaprc.ff99SB
source leaprc.gaff
loadAmberParams CTZ_mod1_112812_prodrg.frcmod
CTZ = loadMol2 CTZ_mod1_112812_prodrg.mol2
saveoff CTZ ctz.lib
receptor = loadPDB rec_nosolv.pdb
#complex = combine {receptor CTZ}
complex = loadPDB com_nosolv.pdb
set default PBRadii mbondi2
saveAmberParm CTZ lig.top lig.crd
saveAmberParm receptor rec.top rec.crd
saveAmberParm complex com.top com.crd
#solvateOct complex TIP3PBOX 15.0
loadamberparams frcmod.ionsjc_tip3p
addions complex Na+ 0
solvatebox complex TIP3PBOX 9.0
saveAmberParm complex com_solvated.top com_solvated.crd
quit
For some reason when I loaded the complex that I had edited by hand (from the pdb from the .rst generated by the the md run) instead of the complex generated by the 'combine' command, the correct topologies were created and the results were printed.
________________________________
From: Chris Chris <alpharecept.yahoo.com>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Friday, February 8, 2013 5:09 PM
Subject: Re: [AMBER] PMEMD amd mmpbsa.py mpi
Thanks Jason,
I have no doubt that you're correct. The solvated complex- in the md production trajectory- has Na+ ions and water. Therefore, the solvated complex I make for the mmpbsa.py MPI should have Na+ ions and water, correct?
In the unsolvated complex- I have no Na+ and no water. This is correct?
Thanks for the help.Just trying to get across the finish line here.
________________________________
From: Jason Swails <jason.swails.gmail.com>
To: Chris Chris <alpharecept.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Friday, February 8, 2013 4:41 PM
Subject: Re: [AMBER] PMEMD amd mmpbsa.py mpi
On Fri, Feb 8, 2013 at 7:08 PM, Chris Chris <alpharecept.yahoo.com> wrote:
> I have been trying to use mmpbsa.py- the MPI version- to analyze the
> binding energy derived from a trajectory obtained using pmemd.
> I keep getting the following error:
>
> Calculations complete. Writing output file(s)...
> Error: Sander output is missing values!
> VDWAALS = ************* EEL = -23028.8786 EGB =
> -4065.0313
> NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
> --clean to erase these files.
> MPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize()
> MPI: aborting job
>
>
> It does indeed go on to write the final .dat file with the results in it,
> however, none of the binding energy values are written- only that it has
> recognized the proper ligand and recpetor masks.
>
> I have seen this problem when searching this forum, but have not yet seen
> a solution for me.
>
> I have generated the topoly files using the following script-run as tleap
> -f script
>
> here is the script:
>
> source leaprc.ff99SB
> source leaprc.gaff
> loadAmberParams CTZ_mod1_112812_prodrg.frcmod
> CTZ = loadMol2 CTZ_mod1_112812_prodrg.mol2
> saveoff CTZ ctz.lib
> receptor = loadPDB 2psj_112812_nowat.pdb
> complex = combine {receptor CTZ}
> set default PBRadii mbondi2
> saveAmberParm CTZ lig.top lig.crd
> saveAmberParm receptor rec.top rec.crd
> saveAmberParm complex com.top com.crd
> loadamberparams frcmod.ionsjc_tip3p
> addions complex Na+ 0
> solvatebox complex TIP3PBOX 9.0
> saveAmberParm complex com_solvated.top com_solvated.crd
> quit
>
> I can see no problems in the pmemd runs. I have looked at the trajectory
> in vmd and all looks well. I have also looked at the .mdout file from the
> production run-again there are no problems.
>
> However, when I look at the complex in VMD- all the bonds seem distorted
> like I didn't use the periodic box option in loading the file. I have tried
> loading aa few forms of the topology file. Nothing seems to work.
>
> I just can't seem to find what's wrong here and think it has something to
> do with pmemd and mmpbsa.py MPI
>
It's highly unlikely that this is caused by the MPI implementation. If you
are getting *s and the spaghetti-mess image when visualizing the
MMPBSA.py-generated trajectories with your topology files, then they are
clearly not compatible (and are causing the error you see).
A couple things to look out for: by default, MMPBSA.py strips all water and
ion residues from the trajectory -- if you have any structural ions or
waters that are present in the 'unsolvated' complex, those will be stripped
from the trajectory and will give rise to the error you're seeing.
If this is indeed the case, you will need to manually set "strip_mask" to
avoid the waters/ions you don't want to delete.
Ultimately this error has to do with an incompatibility between your
topology files, trajectory, and/or the default strip_mask variable. This
error can have numerous root causes and may take awhile to find out what it
is. ParmEd may be able to help here when debugging (as it provides
information about your various topology files).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Feb 09 2013 - 23:00:02 PST
