If you have AmberTools 12 (up to bugfix.1) installed, this is fairly
straightforward to fix using xparmed.py. You can open the topology file
using "xparmed.py", and select the option "printDihedrals". Set :* as the
mask (so you select everything), and print out the full list, looking for
the zeroes.
Then, you can systematically remove those dihedrals using the
"deleteDihedral" command, and that should fix your problem.
However, can you tell what dihedral has periodicity 0 and where that
parameter comes from? It seems like that parameter file should be changed,
wherever it is.
HTH,
Jason
On Tue, Jul 24, 2012 at 4:26 AM, Francesco Pietra <chiendarret.gmail.com>wrote:
> Hi:
> I was running MD without problems for a protein with namd 2.9-cuda,
> amber PARM7 ff (unfortunately I have no access to amber code running
> cuda).
>
> Now, I have inserted a short lipid between two aa, using GAFF params
> for the lipid. Now, minimization could not be carried out: "Error: the
> periodicity of dihedral #249 is zero!"
>
> Here the relevant part of prmtop file, where the said zero is at line
> 3 from the bottom:
> %FLAG DIHEDRAL_PERIODICITY
> %FORMAT(5E16.8)
> 1.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00
> 3.00000000E+00
> 4.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00
> 3.00000000E+00
> 1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00
> 3.00000000E+00
> 1.00000000E+00 2.00000000E+00 3.00000000E+00 1.00000000E+00
> 3.00000000E+00
> 1.00000000E+00 3.00000000E+00 1.00000000E+00 2.00000000E+00
> 3.00000000E+00
> 4.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00
> 4.00000000E+00
> 1.00000000E+00 2.00000000E+00 3.00000000E+00 1.00000000E+00
> 2.00000000E+00
> 3.00000000E+00 4.00000000E+00 3.00000000E+00 2.00000000E+00
> 4.00000000E+00
> 3.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00
> 4.00000000E+00
> 1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00
> 1.00000000E+00
> 2.00000000E+00 3.00000000E+00 4.00000000E+00 2.00000000E+00
> 4.00000000E+00
> 1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00
> 1.00000000E+00
> 2.00000000E+00 3.00000000E+00 4.00000000E+00 1.00000000E+00
> 2.00000000E+00
> 3.00000000E+00 4.00000000E+00 1.00000000E+00 2.00000000E+00
> 3.00000000E+00
> 4.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00
> 4.00000000E+00
> 1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00
> 1.00000000E+00
> 2.00000000E+00 3.00000000E+00 4.00000000E+00 1.00000000E+00
> 2.00000000E+00
> 3.00000000E+00 4.00000000E+00 1.00000000E+00 2.00000000E+00
> 3.00000000E+00
> 4.00000000E+00 2.00000000E+00 2.00000000E+00 1.00000000E+00
> 2.00000000E+00
> 3.00000000E+00 4.00000000E+00 1.00000000E+00 3.00000000E+00
> 2.00000000E+00
> 4.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00
> 4.00000000E+00
> 1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00
> 2.00000000E+00
> 3.00000000E+00 4.00000000E+00 2.00000000E+00 1.00000000E+00
> 2.00000000E+00
> 3.00000000E+00 4.00000000E+00 1.00000000E+00 2.00000000E+00
> 3.00000000E+00
> 4.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00
> 4.00000000E+00
> 2.00000000E+00 4.00000000E+00 1.00000000E+00 2.00000000E+00
> 3.00000000E+00
> 4.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00
> 4.00000000E+00
> 1.00000000E+00 2.00000000E+00 3.00000000E+00 1.00000000E+00
> 2.00000000E+00
> 3.00000000E+00 4.00000000E+00 1.00000000E+00 2.00000000E+00
> 3.00000000E+00
> 4.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00
> 4.00000000E+00
> 1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00
> 1.00000000E+00
> 2.00000000E+00 3.00000000E+00 4.00000000E+00 1.00000000E+00
> 2.00000000E+00
> 3.00000000E+00 4.00000000E+00 1.00000000E+00 2.00000000E+00
> 3.00000000E+00
> 4.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00
> 4.00000000E+00
> 1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00
> 1.00000000E+00
> 3.00000000E+00 4.00000000E+00 2.00000000E+00 1.00000000E+00
> 2.00000000E+00
> 2.00000000E+00 2.00000000E+00 4.00000000E+00 1.00000000E+00
> 2.00000000E+00
> 3.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00
> 4.00000000E+00
> 1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00
> 1.00000000E+00
> 2.00000000E+00 3.00000000E+00 4.00000000E+00 2.00000000E+00
> 2.00000000E+00
> 2.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00
> 4.00000000E+00
> 2.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00
> 4.00000000E+00
> 1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00
> 1.00000000E+00
> 2.00000000E+00 3.00000000E+00 4.00000000E+00 3.00000000E+00
> 1.00000000E+00
> 2.00000000E+00 3.00000000E+00 4.00000000E+00 1.00000000E+00
> 2.00000000E+00
> 3.00000000E+00 4.00000000E+00 2.00000000E+00 2.00000000E+00
> 2.00000000E+00
> 2.00000000E+00 2.00000000E+00 1.00000000E+00 2.00000000E+00
> 3.00000000E+00
> 1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00
> 1.00000000E+00
> 2.00000000E+00 3.00000000E+00 4.00000000E+00 1.00000000E+00
> 2.00000000E+00
> 3.00000000E+00 4.00000000E+00 3.00000000E+00 0.00000000E+00
> 3.00000000E+00
> 1.00000000E+00 2.00000000E+00 1.00000000E+00 2.00000000E+00
> 2.00000000E+00
> 2.00000000E+00
>
>
>
> I am aware that CHARMM27 uses n= 1, 2, 3, 4 in
>
> V DA = V n [ 1 + cos (n ö2 - ö 0 )]
>
> while I don't know if the above zero is allowed in PARM7, or if it is
> an error anyway.
>
> Frankly, I don't know from where to begin to fix the problem, and
> which other data should I produce to get help.
>
> Thanks for your understanding
>
> francesco pietra
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Jul 24 2012 - 05:30:03 PDT
