Jason,
thanks for suggestions again.
The addition of the box dims to the amber chamber have been resulted in the
same error.
in _MMPBSA_complex_gb.mdout.0. I've found
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
FATAL: NATOM mismatch in coord and topology files
it's strange because I've checked number of atoms in all prmtop files and
there were no mismatches (system: 61848 comlpex-dry: 4720, protein 4666,
ligand 54 atoms)
Also I've noticed that _MMPBSA_complex.pdb consist of lipids and ions in
addition to the protein-ligand atoms (although my complex_dry topology
consist of only protein and ligand)
James
2014-04-23 15:18 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
> On Wed, 2014-04-23 at 11:57 +0400, James Starlight wrote:
> > Daniel, Jason thanks for suggestions!
> >
> >
> > I've faced with the problem during mmbpsa calculations due to the some
> > errors in prmtop files. Below I list step-by-step of how each prmtop
> > was obtained.
> >
> >
> > 1) using chamber I've successfully converted charm's psf (solvated
> > system) to the prmtop
> >
> >
> > 2a) using chamber I've successfully converted charm's psf
> > (protein-ligand complex without solvent) to the prmtop
> >
> >
> > than using below command I've got ligand (P0G) and protein prmtops
> > ante-MMPBSA.py -p complex_dry.prmtop -r receptor.prmtop -l
> > ligand.prmtop -n :P0G
> >
> >
> >
> > 2b) using below command I've made another topology of the
> > protein-ligand complex stripped from the solvent (lipids, water and
> > ions)
> > ante-MMPBSA.py -p complex_solvated.prmtop -c complex_dry2.prmtop -s
> > ':POPE|:POPC|:WAT|:POT|:CLA']
> >
> > than using below command I've got ligand (P0G) and protein prmtops
> > ante-MMPBSA.py -p complex_dry2.prmtop -r receptor.prmtop -l
> > ligand.prmtop -n :p0g
>
> These two can be combined into a single step:
>
> ante-MMPBSA.py p complex_solvated.prmtop -c complex_dry2.prmtop \
> -s ':POPE,POPC,WAT,POT,CLA' -r receptor.prmtop -l ligand.prmtop \
> -n :p0g
> >
> >
> > !!!Notice that in the 2b case number of ligand's atoms was bigger
> > (179) that in the 2a case (54 atoms consisted with the charm psf)
>
> This is strange and indicates something is probably wrong. I noticed
> that in the first command you used :P0G whereas in the second command
> you used :p0g (notice the difference in case). Which one is correct?
>
> I would recommend using some of the print* commands in ParmEd
> (printDetails, for instance) to look at some of your mask selections and
> make sure that you are selecting what you intend to select with your
> masks.
> >
> >
> > 3) using below command I've tried to make dG calculations with the
> > tutorial's input file using both topologies obtained from 2a and 2b
> > cases
> > MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
> > complex_solvated.prmtop -cp complex_dry2.prmtop -rp receptor.prmtop
> > -lp ligand.prmtop -y ./dcd/test_md.dcd
> >
> >
> > as the result I've obtained the same error in both cases:
> >
> > CHAMBER prmtops found. Forcing use of sander
> > sander found!
> > Using /home/own/Documents/simulations/amber/amber14/bin/sander
> > cpptraj found!
> > Using /home/own/Documents/simulations/amber/amber14/bin/cpptraj
> > Preparing trajectories for simulation...
> >
> /home/own/Documents/simulations/amber/amber14/bin/MMPBSA_mods/make_trajs.py:631:
> UserWarning: Solvated topology 0 has IFBOX == 0
> > warn('Solvated topology %s has IFBOX == 0' % ifbox)
> > 150 frames were processed by cpptraj for use in calculation.
>
> This happens if you don't give a "-box" flag to chamber. It may not
> matter very much, but it might be worth fixing.
> >
> > Running calculations on normal system...
> >
> > Beginning GB calculations
> > with /home/own/Documents/simulations/amber/amber14/bin/sander
> > calculating complex contribution...
> > File "/home/own/Documents/simulations/amber/amber14/bin/MMPBSA.py",
> > line 96, in <module>
> > app.run_mmpbsa()
> > File
> > "/home/own/Documents/simulations/amber/amber14/bin/MMPBSA_mods/main.py",
> line 218, in run_mmpbsa
> > self.calc_list.run(rank, self.stdout)
> > File
> >
> "/home/own/Documents/simulations/amber/amber14/bin/MMPBSA_mods/calculation.py",
> line 79, in run
> > calc.run(rank, stdout=stdout, stderr=stderr)
> > File
> >
> "/home/own/Documents/simulations/amber/amber14/bin/MMPBSA_mods/calculation.py",
> line 148, in run
> > self.prmtop))
> > CalcError: /home/own/Documents/simulations/amber/amber14/bin/sander
> > failed with prmtop complex_dry2.prmtop!
> > Exiting. All files have been retained.
> >
> >
> > Could it be fixed ?
>
> The error message that will help us diagnose this problem is in
> _MMPBSA_complex_gb.mdout.0. I would need to see that to try and help.
>
> > What #--radii=RADIUS_SET should I define during stripped topology
> > preparation?
>
> This depends on the GB model you want to use. Look at Table 4.1 on page
> 59 of the Amber 14 manual.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Fri Apr 25 2014 - 01:00:02 PDT
