Thanks for your reply,
I will try to upgrade to Ambertools 15. But since the tutorial works just
fine, do you think this could be any issue related to upgrade though? I
will follow your suggestion and see how this goes.
Jag
On Wed, Feb 10, 2016 at 10:37 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> AmberTools 14 is a bit old at this point. You may want to try
> upgrading to AmberTools 15 and see if that helps.
>
> -Dan
>
> On Wed, Feb 10, 2016 at 8:26 AM, Arati Paudyal <apsilwal123.gmail.com>
> wrote:
> > 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
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
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>
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Received on Wed Feb 10 2016 - 08:00:07 PST
