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
!!!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)
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.
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 ? What #--radii=RADIUS_SET should I define during
stripped topology preparation?
James
2014-04-22 18:31 GMT+04:00 Daniel Roe <daniel.r.roe.gmail.com>:
> On Tue, Apr 22, 2014 at 5:16 AM, Jason Swails <jason.swails.gmail.com>
> wrote:
> > This should be "-n :p0g" -- notice the colon. This is the standard
> > Amber mask syntax (used in most Amber programs and described in the
> > Amber manual in one of the Appendices).
>
> A detailed description of atom mask syntax with some examples can be
> found in section "28.2.3. Atom Mask Selection Syntax" (there is also a
> brief description in section 19.1).
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Apr 23 2014 - 04:00:02 PDT
