updated:
I've test both solvated and dry prmtop's made by chamber trying to minimize
my system or run short nvt-equilibration dynamics- and no errors have been
detected during this runs suggesting on proper prmtop's.
On other hand I've faced with the problem during processing of the recults
using the same prmtop's files. E.g
ambpdb -p complex_solvated < minim.rst > minim.pdb
resulted in
-p complex_solvated.prmtop < minim.rst > minim.pdb
| New format PARM file being parsed.
| Version = 1.000 Date = 06/11/03 Time = 12:02:08
ERROR: Flag "TITLE" not found in PARM file
(in that case parm filer consisted of CTITLE pointing on the charm-like
format).
James
2014-04-23 11:57 GMT+04:00 James Starlight <jmsstarlight.gmail.com>:
> 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 - 03:30:02 PDT
