Dear Elvis,
thank you for your reply. I'll reply below and I also have other questions.
I know that the absolute values of these number has no meaning. Indedd, I
am comparing this system with others in which I introduced mutations.
I notice that my output file prints out the following warning:
WARNING: INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIAL
TERMS. THE VALIDITY OF THESE RESULTS ARE HIGHLY QUESTIONABLE
By searching on the web, I found on this post (
http://archive.ambermd.org/201401/0010.html ) that this error is related to
the fact that MMPBSA.py makes sure that bonded interactions (specifically
the BOND, ANGLE, DIHED, and 1-4 nonbonded interactions) completely cancel
out (i.e., in the Final energy differences are zero).
They also say that in a specific case, one can be free to ignore this
warning. This is when tleap deals with improper torsions with 2 atoms of
the same type.In this case , the DIHED contribution to the binding free
energy is negligible (but still has at least one frame larger than the
0.001 kcal/mol cutoff that MMPBSA.py uses to issue a warning). In this
case, one can ignore the warning.
I think that this is my case, since I get:
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 0.0000 0.0000
0.0000
ANGLE 0.0000 0.0001
0.0000
DIHED 0.0013 0.0112
0.0008
I also have two other very important questions:
1. As you suggested, I have introduced the keyword entropy=1, in order to
perform entropy calculations too. I hope this is sufficient for performing
proper delta energy calculations including entropy contribution.
2. I am comparing the calculated energetics with 5 analogous systems in
which I have introduced mutations.
When I introduce only one mutation, the computed eneergetcs differ for ~50
kcal/mol. However, when introducing 5 mutations, I calculate a very high
differences in delta energy (i.e., 274.5471 kcal/mol for the wild type
system, 295.7256 kcal/mol for the system with one mutation, *21371334.3564
kcal/mol for the system with 4 mutatations*) . I obtain the same trend both
with Generalized Born and with Poisson Boltzmann, as well as including and
excluding the entropy term.
Looking at the simulations, I see that in the presence of 4 mutations, the
nucleic acid undergoes relevant conformational changes, even with
distortion of the backbone and fliping out of the bases.
*Can this be a reason of this very huge energy difference??? *Or do you
think that this result is due to some errors in the preparation of the
system? I have used the same input file and checked the topology. Moreover,
the BOND, ANGLE, DIHED contributions are zero (only DIHED = 0.0010).
I hope you have some advises for these issues
Thank you very much
Giulia
2017-06-27 21:25 GMT-07:00 Elvis Martis <elvis.martis.bcp.edu.in>:
> Hi Giulia,
>
> Here are the answers in red ink
>
> By using the GENERALIZED BORN approximation, I get a final Delta
> Energy of *49.3378
> *kcal/mol. Whereas, by using the POISSON BOLTZMANN approximation, I get a
> final Delta Energy of *254.6772* kcal/mol/.
>
> >>> I don't see anything suspicious here considering that you are working
> with protein-protein interactions and such high values can be expected.
> However, these values have no meaning in an absolute sense. Had you changed
> you ligand and then compared the two GB and PB values you would have gotten
> an idea about which of them was a better at binding to the receptor. Have
> you considered the entropy component of binding?? Otherwise, these values
> are just the enthalpy of binding and not the "deltaG(binding)". Moreover, a
> lot depends on what atomic radii you have used (for ex. mbondi2,
> mbondi3.......) and also on what internal dielectric constant you are
> using. Refer to these papers to get more insights into how various tunable
> parameters play a role in the accuracy and reliability of MM-PBSA and
> MM-GBSA calculations.
>
> http://pubs.acs.org/doi/abs/10.1021/ci100275a
>
> http://pubs.rsc.org/-/content/articlelanding/2014/cp/
> c4cp01388c#!divAbstract
>
> http://pubs.acs.org/doi/abs/10.1021/jp404160y
>
> http://pubs.rsc.org/is/content/articlelanding/2016/
> cp/c6cp03670h#!divAbstract
> Moreover, for GB calculations you can consider using various GB models
> [for ex. igb = 1, 2, 5 and 8 (ambertools 16 and above)]
> I would like to ask you if these energies are realistic considering the
> size and characteristics of my system, which are the following: I am
> dealing with an RNA dimer, composed of a total of 3219 atoms (2153 for the
> first monomer, considered as "receptor" and 1066 atoms for the second
> monomer, considered as "ligand"). The original system includes Mg2+ ions
> (co-crystallized) and Na+ ions (used as counterions to balance the charge
> of the system). For the MMPBSA calculation, I have deleted the ions and
> considered the dry receptor, the dry ligand and the dry complex.
> >> It would be very difficult to comment on how realistic these values are
> unless you have some validation sets. Refer to these papers and it will
> guide you through
>
> http://www.sciencedirect.com/science/article/pii/S0022283603006107
>
> http://onlinelibrary.wiley.com/doi/10.1002/jcc.10379/full
>
>
> I see from the post in the mailing list (
> http://archive.ambermd.org/201208/0072.html) that they get unreasonable
> results and that a reasonable value must be of the order of *-200
> *kcal/mol *(negative
> energy) .*
> >> I am afraid I cannot comment anything on that results.
> Can you please advise me on that?
> There is something I am doing wrong in the set-up of the system?
>
> >> I don't see anything wrong in your setup from what you have written.
> Shell I include the ions in the MMPBSA calculation?? And if so, would the
> MMPBSA method still be valid?
>
> >> NO, the mobile ions added for the sake of neutralising the systems
> needs to be deleted and you have correctly followed this.
>
>
> I hope this helps.
>
>
> Best Regards
>
> [photo]
>
>
>
> Elvis Martis
> PhD 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: 27 June 2017 23:23:06
> To: AMBER Mailing List
> Subject: Re: [AMBER] error running mmpbsa
>
> Dear Elvis,
>
> by including these keywords in the following input file (see below), I have
> been able to compete the calculations.
> However, I have a very important question related to the computed energies.
>
> By using the GENERALIZED BORN approximation, I get a final Delta
> Energy of *49.3378
> *kcal/mol. Whereas, by using the POISSON BOLTZMANN approximation, I get a
> final Delta Energy of *254.6772* kcal/mol/.
>
> I would like to ask you if these energies are realistic considering the
> size and characteristics of my system, which are the following: I am
> dealing with an RNA dimer, composed of a total of 3219 atoms (2153 for the
> first monomer, considered as "receptor" and 1066 atoms for the second
> monomer, considered as "ligand"). The original system includes Mg2+ ions
> (co-crystallized) and Na+ ions (used as counterions to balance the charge
> of the system). For the MMPBSA calculation, I have deleted the ions and
> considered the dry receptor, the dry ligand and the dry complex.
>
> I see from the post in the mailing list (
> http://archive.ambermd.org/201208/0072.html) that they get unreasonable
> results and that a reasonable value must be of the order of *-200
> *kcal/mol *(negative
> energy) .*
>
> Can you please advise me on that?
> There is something I am doing wrong in the set-up of the system?
> Shell I include the ions in the MMPBSA calculation?? And if so, would the
> MMPBSA method still be valid?
>
>
> Thank you very much
> Giulia
>
>
>
>
>
> &general
> endframe=200, keep_files=2, interval=10,
> /
> &gb
> igb=2, saltcon=0.100,
> /
> &pb
> istrng=0.100, inp=1, radiopt=0,
> /
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> 2017-06-26 18:18 GMT-07:00 Elvis Martis <elvis.martis.bcp.edu.in>:
>
> > HI,
> >
> > Here PB radii set couldn't find parameters for 3 C5'Cl* not very
> difficult
> > to work around this one.
> >
> > There is an older post here which will help you solve the problem
> > http://archive.ambermd.org/201303/0550.html
> >
> > Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for ...<
> > http://archive.ambermd.org/201303/0550.html>
> > archive.ambermd.org
> > From: Xioling Chuang Date: Thu, 28 Mar 2013 16:56:21 +0100 Dear Jason,
> > Thank you very much for your help. It works fine with setting inp=1 and
> ...
> >
> >
> >
> >
> > 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: 27 June 2017 05:23:59
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] error running mmpbsa
> >
> > 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
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Received on Thu Jun 29 2017 - 12:00:02 PDT
