On Mon, May 07, 2012, Charlotte Siska wrote:
> I have searched the archives and google and was unable to find a
> straightforward explanation as to why I am getting this error when I check
> my parameter and pdb files created by pytleap with ffgbsa:
>
> Reading parm file (test.leap.prm)
> title:
> default_name
>
> mm_options: cut=100
> mm_options: rgbmax=100
> mm_options: diel=C
> mm_options: gb=1
> iter Total bad vdW elect nonpolar genBorn
> frms
> ff: 0 nan 1572822.26 nan inf 0.00 -28376.40
> nan
> id_torus(): Could not find torus for atoms 212 and 6628
The "torus" message is not relevant here, I think. You already have
infinities and "not-a-number" entries before that message.
Best guess is that your structure has two atoms on top of each other. If you
have an inpcrd file (or can create one by running tleap yourself), the
"checkoverlap" command in ptraj can identify bad contacts. If you visualize
the PDB file in a program like VMD or Chimera or xleap, you may also be able
to see problems. Note that your bond, angle and dihedral angle (bad) energy
is also very large, also suggestive of bad coordinates.
It's hard to help without knowing more about your system and its PDB file.
...good luck...dac
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Received on Mon May 07 2012 - 18:30:05 PDT
