in order to help we must know how you generated the prmtop.
On Mon, Sep 17, 2012 at 6:27 AM, Shomesankar Bhunia <
rightclickatrighttime.gmail.com> wrote:
> Hii
> i am using AMBER FF in NAMD and i am getting the following error. The
> problem is in the .prmtop file for which the following error is displayed
>
> *FATAL ERROR: The periodicity of dihedral # 41 is zero!*
> *
> *
> *i looked at the paramtop file and i found that t**he dihedral periodicity
> at 41 is 0 (marked red)*
> *
>
> *
> *
> %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 3.00000000E+00
> 1.00000000E+00
> 3.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00
> 1.00000000E+00
> 2.00000000E+00 3.00000000E+00 3.00000000E+00 1.00000000E+00
> 3.00000000E+00
> 3.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00
> 2.00000000E+00
> 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00
> 2.00000000E+00
> 2.00000000E+00 2.00000000E+00 2.00000000E+00 3.00000000E+00
> 2.00000000E+00
> 0.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00
> 2.00000000E+00
> *
> How to resolve it?
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Received on Mon Sep 17 2012 - 04:00:04 PDT
