What version of Amber are you using? What is the output of
$AMBERHOME/update_amber --version
? I think what's happening here is that the surface area calculation is
failing in cpptraj for some reason (PBSA does not use cpptraj to calculate
the SASA).
HTH,
Jason
On Wed, Feb 10, 2016 at 9:39 AM, Arati Paudyal <apsilwal123.gmail.com>
wrote:
> Deal all,
>
> I have been trying to run MMPBSA/GBSA analysis based on the Advanced Amber
> tutorial posted in the Amber site. I first ran the tutorial using the same
> ras-raf protein complex provided in the tutorial and it ran without any
> problem.
> The problem came when I wanted run my own system (Protein protein complex).
> Even though I used exact same input files and command (except changing
> residue numbers) I am getting some error messages as follows:
>
>
> ................................................................................................................................................
>
> * mmpbsa.in <http://mmpbsa.in>*
>
>
> Input file for running PB and GB
>
> &general
>
> endframe=50, verbose=1,
>
> # entropy=1,
>
> /
>
> &gb
>
> igb=8, saltcon=0.100
>
> /
>
> &pb
>
> inp=1,radiopt=0,istrng=0.100,
>
> /
>
> ~
>
>
>
> $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
> A_B_solvated.prmtop -cp A_B-clean.prmtop -rp A-clean.prmtop -lp
> B-clean.prmtop -y *.mdcrd.gz
>
>
>
> Loading and checking parameter files for compatibility...
>
> mmpbsa_py_energy found! Using
> /opt/software/Amber/14update--Intel-13.0.1.117/bin/mmpbsa_py_energy
>
> cpptraj found! Using
> /opt/software/Amber/14update--Intel-13.0.1.117/bin/cpptraj
>
> Preparing trajectories for simulation...
>
> 50 frames were processed by cpptraj for use in calculation.
>
> Running calculations on normal system...
>
> Beginning GB calculations with
> /opt/software/Amber/14update--Intel-13.0.1.117/bin/mmpbsa_py_energy
>
> calculating complex contribution...
>
> calculating receptor contribution...
>
> File "/opt/software/Amber/14update--Intel-13.0.1.117/bin/MMPBSA.py", line
> 96, in <module>
>
> app.run_mmpbsa()
>
> File
> "/opt/software/Amber/14update--Intel-13.0.1.117/bin/MMPBSA_mods/main.py",
> line 218, in run_mmpbsa
>
> self.calc_list.run(rank, self.stdout)
>
> File
>
> "/opt/software/Amber/14update--Intel-13.0.1.117/bin/MMPBSA_mods/calculation.py",
> line 79, in run
>
> calc.run(rank, stdout=stdout, stderr=stderr)
>
> File
>
> "/opt/software/Amber/14update--Intel-13.0.1.117/bin/MMPBSA_mods/calculation.py",
> line 459, in run
>
> self.prmtop))
>
> CalcError: /opt/software/Amber/14update--Intel-13.0.1.117/bin/*cpptraj
> failed with prmtop A-clean.prmtop!*
>
> Exiting. All files have been retained.
>
>
>
> .............................................................................................................................................
>
>
>
> Simulation and production phases run fine without any problem. But when I
> run the mmpbsa.in command (as above), I get this message saying that one
> of
> my topology files is the problem. If I switch protein A to ligand protein
> (lp) and protein B to receptor protein (rp) then the system goes one more
> step to "calculating ligand contribution" and I will get the same error
> message. So it is clear that the system is pointing out some kind of
> problem with my A-clean.prmtop file but I have no idea
>
>
> i) why that problem is arising
>
>
> ii) how to verify where the problem is??
>
>
> Another thing is, if I remove GB command in mmpbsa.in input file, PBSA
> runs
> fine and also give me the final free energy. So it looks like GB is the
> problem. But it looks weird to me that PB runs fine despite having error
> with one of the topology files because PB uses that topology files as well.
>
>
> I tried another system and I am getting similar error message. So I am
> assuming I am not preparing this individual PDB files properly. Is there
> anything in particular I am missing here???
>
>
> The way I prepared the individual A and B proteins from the complex is:
>
>
> I have complex crystal structure. Then I use Pdb4amber command to clean and
> dry (hydrogens and water). Then I save that as PDB. I open that PDB in
> PyMol and delete sequences for B and save as A and vice versa. Then I run
> tleap to save all teh parameters. Am I doing something wrong here?? Does
> any body have better way to prepare separate PDB from complex???
>
>
>
> So I am very confused on whats going on and how to approach this problem. I
> tried to follow few other posts from past in Amber mailing list but still
> didn't help me that much.
>
>
> I would be very grateful for you input on this issue.
>
>
>
> Jag
>
> Graduate Student, Chemistry, MSU
> _______________________________________________
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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 Wed Feb 10 2016 - 07:30:03 PST
