Dear Elvis,
thank you very much for these useful information. I have checked all files
and it seems that one of the problems was the fact that the trajectory was
in mdcrd format. Using the netcdf format, it seems making at least the GB
calculation.
This is now my command line:
MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -cp tutto.top -rp
azzurro.top -lp rosa.top -y tutto.nc
Let me give you some more information about my system. I am dealing with an
RNA dimer and I want to calculate the binding energy between the two
monomers. As such, I am treating one monomer (the bigger) as the receptor
(azzurro.top), while the other monomeris treated as the ligand (rosa.top).
I have carefully checked that the number of atoms in the azzurro.top + the
number of atoms in the rosa.top equals the total number of atoms in the
topology and in the trajectory of the complex (tutto.top and tutto.nc).
However, as you can see below, I still have problems that seem to be
related to the fact that there is *No radius assigned for atom 3 C5'
CI*
Do you have some insights on how to overcome this issue?
Thank you very much
Giulia
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...
20 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with
/net/software/pkg/amber/amber14-test/bin/mmpbsa_py_energy
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Beginning PB calculations with
/net/software/pkg/amber/amber14-test/bin/mmpbsa_py_energy
calculating complex contribution...
File "/net/software/pkg/amber/amber14-test/bin/MMPBSA.py", line 104, in
<module>
app.run_mmpbsa()
File
"/net/software/pkg/amber/amber14-test/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/net/software/pkg/amber/amber14-test/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/net/software/pkg/amber/amber14-test/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 431, in run
self.prmtop) + '\n\t'.join(error_list) + '\n')
*CalcError: /net/software/pkg/amber/amber14-test/bin/mmpbsa_py_energy
failed with prmtop tutto.top! PB Bomb in pb_aaradi(): No radius assigned
for atom 3 C5' CI*
Exiting. All files have been retained.
2017-06-24 20:35 GMT-07:00 Elvis Martis <elvis.martis.bcp.edu.in>:
> Hi,
>
> one quick question why are your directory names starting with 0??? try
> renaming the directory to start with a letter and number can be pushed at
> the end.
>
> Did you also check that all top files are OK?
>
> the number of atoms in receptor top + ligand top should be equal to
> complex top file and the trajectory file.
>
> Error: Third line contains invalid atom index. >>>>> Check your top file
> for this
> Error: -17.043Error: Could not set up tutto.mdcrd for reading. >>>
> http://archive.ambermd.org/201306/0241.html
>
> Error: Could not set up input trajectory 'tutto.mdcrd'. >>>
> http://archive.ambermd.org/201306/0241.html
>
>
> Hope this helps
>
>
> 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 23:26:40
> To: AMBER Mailing List
> Subject: Re: [AMBER] error running mmpbsa
>
> 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
> > _______________________________________________
> > 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
> >
> _______________________________________________
> 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 26 2017 - 17:00:02 PDT
