On Tue, Jul 24, 2012 at 2:16 PM, Jason Swails <jason.swails.gmail.com> wrote:
> 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.
The only additional params are in a file creating new atom types for
the olefinic carbons in the inserted lipid (trans enone)
-CO-CH=CH-
The carbon of the carbonyl group was then bound to an aa OH, thus
creating an ester bond. The terminal CH of the trans enone was then
bound to an aa side-chain nitrogen. The parametrization of the enone
was adapted from GAFF, creating a new atom type "C2" for the olefinic
carbon, and assuming as "HA" (i.e. as aromatic) their hydrogens. The
file reads:
MASS
C2 12.01 0.00
DIHEDRAL
X -C2 -C2 -X 4 26.600 180.000 2. in analogy with GAFF
NONB
C2 1.9080 0.0860 GAFF c2 and ca OPLS
Additionally, with parmchk I created a frcmod file from the mol2 ff
file for the ensemble of aa inglobating the enone. I parameterized
this four aa ensemble with enone, rather than the enone alone, to take
into account the conform changes. This ensemble was optimized at
HF/6-31G* level, as required for RESP.
I was at updated Ambertools12 and leaprc.ff12SB plus frcmod.ff12SB.
So, in principle, I could try what you suggested above, or wait if you
have further comments on the basis of the above.
Thanks a lot for your kind advice.
francesco
>
> 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 φ2 - φ 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 - 09:00:04 PDT
