Hello,
Thank you for your suggestions. I could use parked.py and xparmed.py to find out which bond had a periodicity 0. However, I could not find out how to add or delete dihedrals b xparmed.py. What is the command for that?
Thanks,
Genzo
> Date: Tue, 15 May 2012 08:57:58 -0700
> From: jason.swails.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] Periodicity errors in pymdsapb
>
> You can use xparmed.py (the GUI version of parmed.py) to query different
> properties (and modify) topology files.
>
> There is a command in parmed.py to print any dihedrals that contain
> specified atoms -- you can use that to find which dihedrals have a
> periodicity of 0.
>
> You can also have xparmed.py delete and/or add dihedrals (allowing you to
> change them directly without going through LEaP again.
>
> HTH,
> Jason
>
> On Tue, May 15, 2012 at 8:36 AM, Genzo Tanaka <gmastanaka.msn.com> wrote:
>
> >
> > Hello, DAC
> > Thank you for your advice.
> > Yes, as you mentioned one of the prmtop file (lig.prm) contained a zero
> > periodicity. However, I can't figure out which bond corresponds to this
> > periodicity.I couldn't identify any bond from the force constant,
> > periodicity, and phase lists. I would appreciate if you could suggest how
> > to find that bond.
> > When building this ligand by xleap, I added to our own parameter file the
> > Lenard-Jones parameters for fluorine along with other bond and angle
> > parameters. As the torsion data for fluorine is defined in "parm10.dat", I
> > did not do anything in our parameter file.
> > The periodicity part of lig.prm looks like this:
> > %FLAG DIHEDRAL_FORCE_CONSTANT%FORMAT(5E16.8) 1.55555556E-01
> > 3.62500000E+00 0.00000000E+00 3.50000000E+00 5.45000000E+00
> > 9.00000000E-01 9.00000000E-01 1.10000000E+00%FLAG
> > DIHEDRAL_PERIODICITY%FORMAT(5E16.8) 3.00000000E+00 2.00000000E+00
> > 2.00000000E+00 2.00000000E+00 2.00000000E+00 0.00000000E+00
> > 2.00000000E+00 2.00000000E+00%FLAG DIHEDRAL_PHASE%FORMAT(5E16.8)
> > 0.00000000E+00 3.14159400E+00 0.00000000E+00 3.14159400E+00
> > 3.14159400E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00
> >
> > Thanks,
> > Genzo
> >
> >
> > > Date: Mon, 14 May 2012 17:54:04 -0400
> > > From: case.biomaps.rutgers.edu
> > > To: amber.ambermd.org
> > > Subject: Re: [AMBER] Periodicity errors in pymdsapb
> > >
> > > On Mon, May 14, 2012, Genzo Tanaka wrote:
> > > >
> > > > A periodicity error occurred during a calculation for the free energy
> > of
> > > > binding in pymdpbsa using a molecular dynamics file from mdnab:
> > > > % pymdpbsa
> > --proj=test,--traj=traj.binpos,--cprm=com.prm,--lprm=lig.prm,
> > > > --rprm=rec.prm,lig=flmfoh1,--start=1,--stop=1000,--step=200,--solv=1,
> > > > --clean &
> > > > % Found an invalid periodicity in the prmtop file: 5
> > >
> > > This is a fatal error that will cause everything after it to fail. It's
> > not
> > > clear (to me, anyway) which prmtop file was being read when the error
> > occured.
> > > But you should look at all three prmtops: go to the DIHEDRAL_PERIODICITY
> > > section, and look at the 6th number (the count starts from 0): that
> > number
> > > is probably zero, which is not a valid value for the periodicity.
> > >
> > > This just starts to localize the problem, but maybe it will help. For
> > > example, you can see which prmtop file is the problem, and which atoms
> > are
> > > involved -- is perhaps the fluorine, where you have your own parameters
> > (I
> > > guess)? Are there also any zero entries for DIHEDRAL_PERIODICITY in any
> > of
> > > the other prmtop files? Basically, we have to find out how/why this
> > entry was
> > > created, in order to have enough information to try to fix it.
> > >
> > > ...good luck...dac
> > >
> > >
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>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Thu May 17 2012 - 09:30:02 PDT
