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
> > > _______________________________________________
> > > 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
> >
> _______________________________________________
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>
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Received on Tue Jun 27 2017 - 11:00:02 PDT
