Hi,
Amber 14 is now 3 years old (2 if the AmberTools component is 15) and
there have been many fixes and improvements to the code since then. I
recommend upgrading to AmberTools 17 (it's free:
http://ambermd.org/AmberTools17-get.html).
-Dan
On Sat, Jun 24, 2017 at 1:56 PM, giulia palermo
<giulia.palermo83.gmail.com> wrote:
> Hi Elvis,
>
> I have tried the MMPBSA calculations with different amber versions and
> sourcing he script, lihe this:
>
> module load amber/14
> source /net/software/src/amber/amber14/amber.sh
>
> MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -cp
> ./0_make_tutto/tutto.top -rp ./0_make_azzurro/azzurro.top -lp
> ./0_make_rosa/rosa.top -y tutto.mdcrd
>
> tutto.mdcrd is the trajetory including receptor and ligand. This trajectory
> is not solvated.
> I have checked this trajectory and it is compatible with the prmtop file
> (tutto.top).
>
> However, I get the following error (with all AMBER versions I used), which
> is related to the fact that cpptraj can not query tutto.mdcrd. Can you
> please give me some advice on what is going on?
> I also report below my MMPBSA input file.
>
> Thank you
> Giulia
>
>
>
> ---- ERROR :
> Loading and checking parameter files for compatibility...
> mmpbsa_py_energy found! Using
> /net/software/src/amber/amber14/bin/mmpbsa_py_energy
> cpptraj found! Using /net/software/src/amber/amber14/bin/cpptraj
> Preparing trajectories for simulation...
> Error: Third line contains invalid atom index.
> Error: -17.043Error: Could not set up tutto.mdcrd for reading.
> Error: Could not set up input trajectory 'tutto.mdcrd'.
> File "/net/software/src/amber/amber14/bin/MMPBSA.py", line 103, in
> <module>
> app.file_setup()
> File
> "/net/software/src/amber/amber14/lib/python2.7/site-packages/MMPBSA_mods/main.py",
> line 156, in file_setup
> self.mpi_size, str(external_progs['cpptraj']), self.pre)
> File
> "/net/software/src/amber/amber14/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py",
> line 66, in make_trajectories
> traj = Trajectory(FILES.complex_prmtop, FILES.mdcrd, cpptraj)
> File
> "/net/software/src/amber/amber14/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py",
> line 467, in __init__
> self.Query()
> File
> "/net/software/src/amber/amber14/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py",
> line 602, in Query
> raise TrajError('%s failed when querying %s' % (self.exe, traj))
> *TrajError: /net/software/src/amber/amber14/bin/cpptraj failed when
> querying tutto.mdcrd*
> Exiting. All files have been retained.
>
>
> ---- MMPBSA input file
>
> &general
> endframe=200, keep_files=2, interval=10,
> /
> &gb
> igb=2, saltcon=0.100,
> /
> &pb
> istrng=0.100,
> /
>
>
>
> 2017-06-23 20:43 GMT-07:00 Elvis Martis <elvis.martis.bcp.edu.in>:
>
>> Sorry,
>>
>> I meant without quotes
>>
>>
>> Best Regards
>>
>> [photo]
>>
>>
>>
>> Elvis Martis
>> Ph.D. Student (Computational Chemistry)
>> at Bombay College of Pharmacy
>>
>>
>> A Kalina, Santacruz [E], Mumbai 400098, INDIA
>> W www.elvismartis.in<https://webapp.wisestamp.com/www.elvismartis.in>
>> Skype. adrian_elvis12<https://webapp.wisestamp.com/#>
>>
>>
>> [https://ci3.googleusercontent.com/proxy/P0F8-p0kwxKdscp6zsT-
>> ZSRttk9OJEsBGiaXej_H2ERz8n2ma5SLHFAWJdKL-wqOlXSGjbmEyga9C8lmU1bs-_
>> yPIq3CnazA5eJVDYjce1r-34uwxqjjRnmAtE473lEq28nSHQ=s0-
>> d-e1-ft#https://s3.amazonaws.com/images.wisestamp.com/
>> icons_for_colors_32/linkedin.png]<http://www.linkedin.com/
>> in/elvisadrianmartis/>
>>
>>
>>
>>
>>
>> ________________________________
>> From: Elvis Martis <elvis.martis.bcp.edu.in>
>> Sent: 24 June 2017 06:39:56
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] error running mmpbsa
>>
>> HI,
>>
>> Try this command before you run you mm_pbsa.py
>>
>> "source <path_to_amber_home>/amber.sh" for bash with quotes
>>
>> or
>>
>> "source <path_to_amber_home>/amber.csh" for csh with quotes
>>
>>
>> Best Regards
>>
>> [photo]
>>
>>
>>
>> Elvis Martis
>> Ph.D. Student (Computational Chemistry)
>> at Bombay College of Pharmacy
>>
>>
>> A Kalina, Santacruz [E], Mumbai 400098, INDIA
>> W www.elvismartis.in<https://webapp.wisestamp.com/www.elvismartis.in>
>> Skype. adrian_elvis12<https://webapp.wisestamp.com/#>
>>
>>
>> [https://ci3.googleusercontent.com/proxy/P0F8-p0kwxKdscp6zsT-
>> ZSRttk9OJEsBGiaXej_H2ERz8n2ma5SLHFAWJdKL-wqOlXSGjbmEyga9C8lmU1bs-_
>> yPIq3CnazA5eJVDYjce1r-34uwxqjjRnmAtE473lEq28nSHQ=s0-
>> d-e1-ft#https://s3.amazonaws.com/images.wisestamp.com/
>> icons_for_colors_32/linkedin.png]<http://www.linkedin.com/
>> in/elvisadrianmartis/>
>>
>>
>>
>>
>>
>> ________________________________
>> From: giulia palermo <giulia.palermo83.gmail.com>
>> Sent: 24 June 2017 02:02:54
>> To: AMBER Mailing List
>> Subject: [AMBER] error running mmpbsa
>>
>> Dear all,
>>
>> I am doing some MMPBSA calculations using the dollowing input and command
>> line:
>>
>> --- mmpbsa.inp
>> &general
>> endframe=2201, keep_files=2, interval=6,
>> /
>> &gb
>> igb=2, saltcon=0.100,
>> /
>> &pb
>> istrng=0.100,
>> /
>>
>> --- command line
>> MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -cp
>> ./0_make_tutto/tutto.top -rp ./0_make_azzurro/azzurro.top -lp
>> ./0_make_rosa/rosa.top -y tutto.mdcrd
>>
>> However, the calculation crashes and I am having the following error:
>>
>> Loading and checking parameter files for compatibility...
>> mmpbsa_py_energy found! Using
>> /net/software/pkg/amber/amber14-test/bin/mmpbsa_py_energy
>> cpptraj found! Using /net/software/pkg/amber/amber14-test/bin/cpptraj
>> Preparing trajectories for simulation...
>> Error: Third line contains invalid atom index.
>>
>> *Error: -17.043Error: Could not set up tutto.mdcrd for reading.Error:
>> Could not set up input trajectory 'tutto.mdcrd'.*
>> File "/net/software/pkg/amber/amber14-test/bin/MMPBSA.py", line 103, in
>> <module>
>> app.file_setup()
>> File
>> "/net/software/pkg/amber/amber14-test/lib/python2.7/
>> site-packages/MMPBSA_mods/main.py",
>> line 156, in file_setup
>> self.mpi_size, str(external_progs['cpptraj']), self.pre)
>> File
>> "/net/software/pkg/amber/amber14-test/lib/python2.7/
>> site-packages/MMPBSA_mods/make_trajs.py",
>> line 66, in make_trajectories
>> traj = Trajectory(FILES.complex_prmtop, FILES.mdcrd, cpptraj)
>> File
>> "/net/software/pkg/amber/amber14-test/lib/python2.7/
>> site-packages/MMPBSA_mods/make_trajs.py",
>> line 467, in __init__
>> self.Query()
>> File
>> "/net/software/pkg/amber/amber14-test/lib/python2.7/
>> site-packages/MMPBSA_mods/make_trajs.py",
>> line 602, in Query
>> raise TrajError('%s failed when querying %s' % (self.exe, traj))
>> TrajError: /net/software/pkg/amber/amber14-test/bin/cpptraj failed when
>> querying tutto.mdcrd
>> Exiting. All files have been retained.
>>
>>
>> I have successfully preformed MMPBSA calculations in the past and I can not
>> understand what is gouing wrong.
>> It seems that it can not read the trajectory of the complex. But I have
>> checked it and it seems OK.
>> Do you have any idea?
>>
>> thank you
>>
>> Giulia
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
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>>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Mon Jun 26 2017 - 06:00:08 PDT
