Hi,
I would say it's only an issue if the tutorial stopped working after
the upgrade. Without knowing more details about your system it's tough
to say what might be going wrong. What is certain is that there were
many improvements made between AmberTools 14 and 15, and upgrading may
solve your problem. If it does not however please let us know.
Good luck,
-Dan
On Wed, Feb 10, 2016 at 8:53 AM, Arati Paudyal <apsilwal123.gmail.com> wrote:
> 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)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
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> 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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Received on Wed Feb 10 2016 - 08:30:03 PST
