The delete dihedrals function for xparmed.py was added as part of bugfix.1
for AmberTools12. You will need to apply the patch and re-compile.
-Bill
On Thu, May 17, 2012 at 12:02 PM, Genzo Tanaka <gmastanaka.msn.com> wrote:
>
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Fri May 18 2012 - 12:00:03 PDT
