Re: [AMBER] trajout or mask pdb with connection records (title is wrong, see this one)

From: Jason Swails <>
Date: Tue, 3 Nov 2015 08:06:44 -0500

On Mon, Nov 2, 2015 at 9:55 PM, windy <> wrote:

> Hi, everyone,
> How do amber trajout pdb with connectivity records? Are there any
> solutions?

​There is no option for this in Amber right now.

> For my trajectory has a user-defined new residue (like phosphorylation
> and so on), when I trajout one frames to PDB (no connection records) and
> furthur QM/MM calculation in Gaussian, the Gaussian software often judge
> the wrong connection, especially the amino acid with benzene ring (PHE,
> usually the 1.5 bonding and 2.0 bonding).
> I further using Discovery or Sybyl to read the original PDBs from Amber
> to generate the connection records, but the connectivity records is
> disruptted around the user-defined new residues (no complete connection
> records generate).
> Are there any solutions to generate the complete connection records from
> Amber?

​Not that I know of.

An idea might be to write a mol2 file (or something else that explicitly
stores bonds), then see if a conversion program (maybe something like
openbabel) will write a PDB file with CONECT records.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Nov 03 2015 - 05:30:03 PST
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