Adding to what Bill said, if there's no CONECT cards explicitly present in
the structure (if it's a PDB), then visualization programs have to rely on
their own definitions of what constitutes a "bond" of any order. Thus, the
differing "results" from different molecule viewers.
"Double bonds", "single bonds", and "triple bonds" are only distinguished in
molecular simulation based on their bond strength and equilibrium bond
distances, so there's no reason for amber files to track a formal "bond
order" during molecular simulations. Some programs, like antechamber and I
believe tleap/xleap, have a definition for bond order, but that's only used
to determine force constants, and equilibrium values (via setting atom
types).
Good luck!
Jason
On Sat, Oct 9, 2010 at 3:59 PM, Computational Chemist <
computationalchemist.ymail.com> wrote:
> Dear Amber users,
>
> I am simulating a protein with non standard residue. I built the ligand
> structure using CASHE software and saved the structure as mol2 or pdb file.
> I used antechamber and gaff force field to get the necessary parameters. My
> question is how can I check the geometry of my ligand after calculations?
>
> I used vmd and chimera, the structures look good but there is no way
> to make sure that double and single bonds are correct. However, when I
> used CASHE or Gaussian view to look at the pdb structure , each program
> gives me a structure with weired bonds different from each other and from
> the one I built and wanted. I even looked at the sustiva.pdb structure
> "tutorial4b" in gaussian view, it gives me disconnected molecule. The pdb
> structures don't have any information about the bond kind, So How do I
> figure out whether my calculations have the correct ligand structure or not?
>
> Thank you,
> Darine
>
>
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sat Oct 09 2010 - 18:30:02 PDT
