Hi Qi,
I looked at the files you sent me, and I see that the GB calculations
finish successfully and the PB calculations don't. However, like you
mentioned, the PB output files do not contain any error messages, so
there's no way of knowing exactly what's going wrong.
You are just running the tutorial (Ras-Raf binding) with the same input
files that the tutorial website shows, is that correct? Given your output
files, the nab executable is being used to extract energies from your
trajectory, which means the entire calculation is being done via AmberTools
12 -- not Amber 11.
I tried running the tutorial files on my machine, and it completed without
error. Unless you made changes to the files downloaded from the tutorial
website, my guess is that differences with your OS and/or compilers are
revealing a subtle bug somewhere (my guess is more on the compilers than it
is on the OS).
Can you provide the compilers and OS that you're using to build AmberTools
12 so that we may be able to track down why your calculation is failing?
Without being able to reproduce the error you're seeing, we will have
trouble tracking down the problem.
As a reference, each frame should take ~300 MB of RAM (at least that's what
it did on my machine). If you are running in parallel (say, for instance,
on 12 threads), you will need 12 threads * 300 MB/thread ~= 3.5 GB of
available RAM to run your calculation. If you are running on a cluster
that uses some kind of resource manager (like PBS or torque), and you
haven't requested as much RAM as Amber tries to use, the scheduler may
silently kill your simulation with a potentially obscure message related to
using more resources than permitted, but this is just speculation.
Also, if you were running parallel (which it doesn't look like you were),
try running in serial to see if you reproduce the same error.
Hope this helps,
Jason
On Thu, Jun 28, 2012 at 9:53 AM, qiqi <hova.1985.yahoo.com.cn> wrote:
> Hi Jason,
>
>
> I have already sent you the _MMPBSA_* files, I'm not sure whether you have
> received it.
> Thank you very much!
>
>
> All the best,
> Qi
>
>
> --- 12年6月26日，周二, Jason Swails <jason.swails.gmail.com> 写道：
>
>
> 发件人: Jason Swails <jason.swails.gmail.com>
> 主题: Re: [AMBER] Problem while running MMPBSA
> 收件人: "AMBER Mailing List" <amber.ambermd.org>
> 日期: 2012年6月26日,周二,上午1:09
>
>
> It doesn't appear that you're trying to run decomp analysis, since your
> output file appears to be NAB output from mmpbsa_py_energy. In this case,
> the advice on that thread does not apply. Can you zip up your _MMPBSA_*
> files and attach them so we can take a look?
>
> All the best,
> Jason
>
> On Mon, Jun 25, 2012 at 11:33 AM, qiqi <hova.1985.yahoo.com.cn> wrote:
>
> > Hi,
> >
> > I found a similar problem in the mailing list:
> > http://archive.ambermd.org/201206/0122.html
> > The suggestion is :" remove the dec_verbose variable from the
> > MMPBSA_pb.mdin
> > file and then re-run the MMPBSA.py command line with the -use-mdins flag
> at
> > the end"
> > However, I didn't find the dec_verbose variable in my _MMPBSA_pb.mdin
> file.
> >
> > I tried to found out which subroutine is wrong. I just found the error
> > messages as in my last mail:
> > CalcError: /shared/build/amber12/bin/mmpbsa_py_energy failed with prmtop
> > ras-raf.prmtop!
> > Processing ASCII trajectory (_MMPBSA_complex.mdcrd.0)
> > Processing frame 1
> > iter Total bad vdW elect nonpolar EPB frms
> >
> > By the way, I am using Ambertools12 and Amber11.
> > It will be great if you could give some more advice to solve the problem.
> > Thank you very much!
> >
> > Best,
> > Angela
> >
> >
> >
> > --- 12年6月23日，周六, Jason Swails <jason.swails.gmail.com> 写道：
> >
> >
> > 发件人: Jason Swails <jason.swails.gmail.com>
> > 主题: Re: [AMBER] Problem while running MMPBSA
> > 收件人: "AMBER Mailing List" <amber.ambermd.org>
> > 日期: 2012年6月23日,周六,上午7:26
> >
> >
> > Usually when PB quits, there is some kind of error message about what
> > subroutine it bombed out in. Do you see any information like that?
> > Without this information we will probably not be able to help.
> >
> > All the best,
> > Jason
> >
> > On Fri, Jun 22, 2012 at 4:33 PM, qiqi <hova.1985.yahoo.com.cn> wrote:
> >
> > > Hi Jason,
> > >
> > > Thank you very much for your help, the problem is solved.
> > > However I met another problrm while running the example.
> > > Here are the error message:
> > > *******************************************************************
> > > $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat
> -sp
> > > ras-raf_solvated.prmtop -cp ras-raf.prmtop -rp ras.prmtop -lp
> raf.prmtop
> > -y
> > > *.mdcrd
> > > Reading command-line arguments and input files...
> > > Loading and checking parameter files for compatibility...
> > > mmpbsa_py_energy found! Using
> /shared/build/amber12/bin/mmpbsa_py_energy
> > > cpptraj found! Using /shared/build/amber12/bin/cpptraj
> > > Preparing trajectories for simulation...
> > > 50 frames were processed by cpptraj for use in calculation.
> > >
> > > Beginning GB calculations with
> /shared/build/amber12/bin/mmpbsa_py_energy
> > > calculating complex contribution...
> > > calculating receptor contribution...
> > > calculating ligand contribution...
> > >
> > > Beginning PB calculations with
> /shared/build/amber12/bin/mmpbsa_py_energy
> > > calculating complex contribution...
> > > CalcError: /shared/build/amber12/bin/mmpbsa_py_energy failed with
> prmtop
> > > ras-raf.prmtop!
> > > Exiting. All files have been retained.
> > > *********************************************************
> > > vi _MMPBSA_pb.mdin
> > > PB
> > > npbopt = 0
> > > istrng = 0.1
> > > bcopt = 5
> > > inp = 2
> > > accept = 0.001
> > > cavity_offset = -0.5692
> > > maxitn = 1000
> > > fillratio = 4.0
> > > iprob = 2.0
> > > space = 0.5
> > > eneopt = 2
> > > dprob = 1.4
> > > radiopt = 1
> > > dbfopt = 1
> > > epsin = 1.0
> > > nfocus = 2
> > > cutnb = 0
> > > epsout = 80.0
> > > fscale = 8
> > > solvopt = 1
> > > smoothopt = 1
> > > sprob = 0.557
> > > cavity_surften = 0.0378
> > >
> ************************************************************************
> > > vi _MMPBSA_complex_pb.mdout.0
> > > Reading parm file (ras-raf.prmtop)
> > > title:
> > >
> > > mm_options: e_debug=3
> > > mm_options: ipb=2
> > > mm_options: inp=2
> > > mm_options: epsin=1.000000
> > > mm_options: epsout=80.000000
> > > mm_options: smoothopt=1
> > > mm_options: istrng=100.000000
> > > mm_options: radiopt=1
> > > mm_options: dprob=1.400000
> > > mm_options: iprob=2.000000
> > > mm_options: npbopt=0
> > > mm_options: solvopt=1
> > > mm_options: accept=0.001000
> > > mm_options: maxitn=1000
> > > mm_options: fillratio=4.000000
> > > mm_options: space=0.500000
> > > mm_options: nfocus=2
> > > mm_options: fscale=8
> > > mm_options: bcopt=5
> > > mm_options: eneopt=2
> > > mm_options: cutnb=0.000000
> > > mm_options: sprob=0.557000
> > > mm_options: cavity_surften=0.037800
> > > mm_options: cavity_offset=-0.569200
> > > Processing ASCII trajectory (_MMPBSA_complex.mdcrd.0)
> > >
> > > Processing frame 1
> > > iter Total bad vdW elect nonpolar EPB frms
> > > ************************************************************
> > >
> > > Anyone can help me or give me some advice.
> > > Thanks
> > >
> > > Angela
> > >
> > >
> > > --- 12年6月21日，周四, Jason Swails <jason.swails.gmail.com> 写道：
> > >
> > >
> > > 发件人: Jason Swails <jason.swails.gmail.com>
> > > 主题: Re: [AMBER] Problem while running MMPBSA
> > > 收件人: "AMBER Mailing List" <amber.ambermd.org>
> > > 日期: 2012年6月21日,周四,上午2:08
> > >
> > >
> > > Then use MMPBSA.py (note the .py at the end) from AmberTools 12, rather
> > > than MMPBSA (the version from AmberTools 1.5).
> > >
> > > Do you get the same error?
> > >
> > > HTH,
> > > Jason
> > >
> > > On Wed, Jun 20, 2012 at 1:32 PM, qiqi <hova.1985.yahoo.com.cn> wrote:
> > >
> > > > Hi,
> > > >
> > > > I am using Amber11 and I have already built the latest Ambertools.
> > > >
> > > > Best wishes,
> > > >
> > > > Angela
> > > >
> > > >
> > > > --- 12年6月21日，周四, Jason Swails <jason.swails.gmail.com> 写道：
> > > >
> > > >
> > > > 发件人: Jason Swails <jason.swails.gmail.com>
> > > > 主题: Re: [AMBER] Problem while running MMPBSA
> > > > 收件人: "AMBER Mailing List" <amber.ambermd.org>
> > > > 日期: 2012年6月21日,周四,上午1:19
> > > >
> > > >
> > > > Can you try upgrading to AmberTools 12 and try the version of
> MMPBSA.py
> > > > included there?
> > > >
> > > > All the best,
> > > > Jason
> > > >
> > > > On Wed, Jun 20, 2012 at 12:08 PM, qiqi <hova.1985.yahoo.com.cn>
> wrote:
> > > >
> > > > > Hi all,
> > > > >
> > > > >
> > > > > I met a problem while runnin MMPBSA, even trying to run the
> tutorial
> > > > > examples.
> > > > > The error message are as followed.
> > > > > Can anyone give me some advice about how to solve this problem.
> > > > > Thanks.
> > > > >
> > > > >
> > > > > MMPBSA -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
> > > > > ras-raf_solvated.prmtop -cp ras-raf.prmtop -rp ras.prmtop -lp
> > > raf.prmtop
> > > > -y
> > > > > *.mdcrd
> > > > >
> > > > > Reading command-line arguments and input files...
> > > > > Loading and checking parameter files for compatibility...
> > > > > ptraj found! Using /shared/build/amber11/bin/ptraj
> > > > > mmpbsa_py_energy found! Using
> > > /shared/build/amber11/bin/mmpbsa_py_energy
> > > > > for GB calculations
> > > > > mmpbsa_py_energy found! Using
> > > /shared/build/amber11/bin/mmpbsa_py_energy
> > > > > for PB calculations
> > > > > Preparing trajectories for simulation...
> > > > > sh: line 1: 24583 Floating point
> > > exception/shared/build/amber11/bin/ptraj
> > > > > ras-raf.prmtop _MMPBSA_complexinpcrd.in > _MMPBSA_ptraj4.out 2>&1
> > > > > sh: line 1: 24589 Floating point
> > > exception/shared/build/amber11/bin/ptraj
> > > > > ras.prmtop _MMPBSA_receptorinpcrd.in > _MMPBSA_ptraj5.out 2>&1
> > > > > sh: line 1: 24591 Floating point
> > > exception/shared/build/amber11/bin/ptraj
> > > > > raf.prmtop _MMPBSA_ligandinpcrd.in > _MMPBSA_ptraj6.out 2>&1
> > > > > 2 frames were read in and processed by ptraj for use in
> calculation.
> > > > >
> > > > > Beginning GB calculations with mmpbsa_py_energy...
> > > > > calculating complex contribution...
> > > > > getpdb: can't open file _MMPBSA_complex.pdb
> > > > > Error: mmpbsa_py_energy error during GB calculations!
> > > > > NOTE: All files have been retained for debugging purposes. Type
> > > MMPBSA.py
> > > > > --clean to erase these files.
> > > > >
> > > > >
> > > > > Angela
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Jason M. Swails
> > > > Quantum Theory Project,
> > > > University of Florida
> > > > Ph.D. Candidate
> > > > 352-392-4032
> > > > _______________________________________________
> > > > 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
> > > >
> > >
> > >
> > >
> > > --
> > > Jason M. Swails
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Candidate
> > > 352-392-4032
> > > _______________________________________________
> > > 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
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > 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
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> 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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Jul 01 2012 - 19:30:03 PDT
