Dear Carlos,
I have carried a GAMESS geometry optimization using GAMESS. I have used
the gamess output (log file) to fit RESP charges using RED-vIII.5 tools
and finally i generated a *.mol2 file that i used in the generation of
.prmtop and .inpcrd files by the same way as shown in tutorial B4 at amber
tutorials (
http://ambermd.org/tutorials/basic/tutorial4b/).
I used GAFF and used Leap in the generation of the .prmtop and .inpcrd
files.Thanks in advance.
On Mon, Sep 17, 2012 at 4:09 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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 - 04:30:03 PDT
