Dear Jason,
Thank you so much for your reply. The version is:
Version is reported as <version>.<patches applied>
AmberTools version 14.27
Amber version 14.12
Could you please help me to diagnose these issues? I can send you the PDB
and prmtop files if that helps to diagnose any problems. I have tried every
other resources and helps around campus and apparently everybody told me to
restart the process again, which I don't see the point here. So any input
from your side would be highly appreciated.
Jag
On Wed, Feb 10, 2016 at 10:12 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
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>
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Received on Wed Feb 10 2016 - 07:30:05 PST
