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 Wed Apr 23 2014 - 07:30:03 PDT
