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/#>
[
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________________________________
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
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Received on Fri Jun 23 2017 - 21:00:03 PDT
