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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Received on Tue May 15 2012 - 09:00:02 PDT
