Re: [AMBER] Does AMBER ignore CONECT information in pdb input?

From: Jason Swails <jason.swails.gmail.com>
Date: Mon, 6 Feb 2012 23:32:52 -0500

Parts of amber listens to CONECT records -- like leap and cpptraj (I think), which stores the bonding information properly. However, ambpdb does _not_ write CONECT records in PDBs that it generates (I don't think any program in Amber _writes_ CONECT records, just reads them).

Thus, most visualization programs will be left to guess which bonds exist and will use some sort of distance cutoff criteria. This does not mean those are the bonds stored in the topology file. If you want to see the actual connectivity in your prmtop, then load that as a new molecule in VMD and load your pdb as a frame in that molecule.

That makes VMD use the bonding info in the prmtop instead of guessing.

HTH,
Jason

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On 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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Received on Mon Feb 06 2012 - 21:00:02 PST