On Thu, 2014-05-22 at 07:59 -0700, zahra khatti wrote:
> Dear amber users
>
> I want to calculate binding free energy with mmpbsa, but I get this error:
>
> Found an invalid periodicity in the prmtop file: 0
> CalcError: /user/local/amber12/bin/mmpbsa_py_energy failed with prmtop BNNTnew.prmtop!
>
> where BNNTnew.prmtop is the complex file in my case,
>
> as well as I added parameters to frcmod for simulation, Is it related to this error?
Check your frcmod file that you used. Do you see lines that are filled
with zeroes and say something like "ATTN: needs revision"?
If so, you need to fill in parameters for these terms.
A torsion term with a periodicity of 0 is not technically "wrong", but
it is completely useless. With a periodicity of 0, the torsion term
turns into a constant added to the energy (whose gradient, of course, is
0 so it has no effect on forces or dynamics).
The preferred way to "delete" a dihedral (that is, so it does not
contribute to the potential) is to set the force constant (only) to zero
(since then it doesn't add an arbitrary constant to the energy). This
is appropriate in situations where the existing bonded and nonbonded
terms reproduce the desired torsion profile without needing to add an
additional fitting parameter.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu May 22 2014 - 09:00:02 PDT
