I'm fairly certain that AMBER ignores any such information in the pdb. If
you are making prmtop and inpcrd files from a pdb you need to make sure
that the forcefield you are loading has definitions for everything in your
pdb, or else load a library that contains the missing information. You can
use the edit function in xleap to check your structure and see if the bonds
you intend are present.
What program are you using to visualize your pdb afterwards? Programs like
PyMol will make assumptions about covalent bonds based on distance
information. Therefore, if your structure is insufficiently relaxed
(atomic clashes) you will see bonds in the wrong places. If you have been
using PyMol maybe swap to VMD instead.
~Aron
On Mon, Feb 6, 2012 at 11:05 PM, Chinh Su Tran To
<chinh.sutranto.gmail.com>wrote:
> Dear Amber users,
>
> Is it correct that AMBER ignores all CONECT information in the pdb input?
> What happens if the pdb contains the small molecules?
>
> It happened to me that when I convert the prmtop and inpcrd files back to
> pdb formatted file using "ambpdb", the structure does not look right to me
> (containing wrong connection or bonds), then I also converted the
> after_minimization_structure, it looked better but still contained wrong
> bonds (e.g 5 connections for a C atom), and after all, my
> equilibration_structure's totally wrong.
>
> Could I ask for any help to explain how it could be? Any clue to avoid/fix
> it?
>
> Thank you.
>
> Chinsu
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 06 2012 - 20:30:02 PST
