Hi Giulia,
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.
>>>>> If you are using a single trajectory approach for MMPBSA then the internal energies cancel each other. this is just warning and you can ignore as it also says.
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.
>>> I guess you are good here.
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
>>>>>> The energy value with 4 mutations is rediculously large, personally haven't encountered such large values. These are using PB or GB calculations. For PB, the results are sensitive to what internal dieclectric constant you have used. There are good lot of papers to serve as a guide.
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.
>> I am not the right person to comment on this, but have you performed 2-3 parallel simulations (with different seed number)?? and do you see the same observation??
*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 believe you are using single trajectory approach, if what I believe is true then "the BOND, ANGLE, DIHED contributions are zero (only DIHED = 0.0010)" is true.
Can you tell, in more details, how you performed you MM-PB/GB-SA results?
Input and log files will help.
Best Regards
Elvis Martis
Mumbai, INDIA.
________________________________________
From: giulia palermo <giulia.palermo83.gmail.com>
Sent: 30 June 2017 00:20:00
To: AMBER Mailing List
Subject: Re: [AMBER] error running mmpbsa
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 Mon Jul 03 2017 - 00:00:02 PDT
