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
>>
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--
-------------------------
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 - 08:00:03 PST
