Dear Aron,
It is true. I visualized it in Pymol. Thanks for the suggestion.
I used the ff99SB and gaff to run again MD for my docked complexes. I'd
have checked it with xleap.
Just one thing Im wondering, how AMBER turns to "understand" what bond (in
small molecules) it should make?
Thank you.
Chinsu
On Tue, Feb 7, 2012 at 12:18 PM, Aron Broom <broomsday.gmail.com> wrote:
> 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
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
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Received on Mon Feb 06 2012 - 21:30:03 PST
