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
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Jun 24 2017 - 21:00:03 PDT
