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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>
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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 Tue May 15 2012 - 09:00:03 PDT
