Regarding mismatches in the ligand atoms topology made by 2 different
cases- it's possible that some addition hydrogens have been added to the
ligand (e.g from the lipids) during topology conversion.
Please provide me with the short examples for the parmed.py -p
complex_solvated.prmtop
which will (1) remove of all atoms from the complex_solvated.prmtop
topology but only not the ligand (it correspond to the mask name :P0G) and
(2) remove lipids, water and ions from the complex_solvated.prmtop
(corresponded to the ':POPE|:POPC|:WAT|:POT|:CLA' ) including all
hydrogen's from those residues resultiong in the protein-ligand.prmtop
James
2014-04-25 11:27 GMT+04:00 James Starlight <jmsstarlight.gmail.com>:
> 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 - 01:00:03 PDT
