Bill,
Thank you for your help. The "Delete dihedrals" is in the list of options.
Thanks,
Genzo
> Date: Fri, 18 May 2012 14:38:41 -0400
> From: brmilleriii.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] Periodicity errors in pymdsapb
>
> 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
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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 Tue May 22 2012 - 09:30:11 PDT
