Re: [AMBER] xleap, unit connectivity and atom name

From: David A. Case <>
Date: Wed, 17 Jul 2013 10:39:28 -0400

On Wed, Jul 17, 2013, Rasha Alqus wrote:
> I have a structure that is formed a units I called GRA, I used
> antechamber to produce mol2 file and frcmond then I loaded them in xleap
> and I created this unit, I have checked this unit and every thing is
> okey , then saved lib,crd,top.pdb. Then I used this unit to produce my
> structure using combine command then connected the units together using
> exleap,

This is not the recommended procedure. Most of the time you are better off
creating a pdb file of the combined system, and using the loadPdb command to
read things into leap. This in effect creates the combined unit.

I saved mol2 file and lib for big structure and I checked its
> unit and every thing okey. The problem that the connectivity between
> the unit are sp2 (atom type) ca, and it seem that when I draw these
> bond and relax my system these bond are not ar,

The bond identifications in the mol2 file are not used in Amber. Other
programs (like visualization programs) might use these to decide how to draw
bonds, but the Amber force field doesn't have the concept of a "bond type"

> The prablom when I load the pdb file in xleap
> ( in leaprc I loaded gaff force field and lib), xleap shows that the
> big structure the units are not connected togather, even thougth I have
> checked its unit and all are connected with the right bond type.

I'm not sure how this can happen. You can use the desc command in LEaP to
see what bonds are present; or you can use ParmEd to examine the resulting
prmtop file to get access to the same information.

> I visualized the pdb using vmd and all unites are connected.

This doesn't mean anything: given a pdb file, vmd draws bonds based on
distances, *not* on whether the force field has a bond. If you load the
prmtop file into vmd first, then it will draw exactly the bonds that are in
the prmtop file (so this path is yet another way to see if you are getting
what you want in the end.

> I have another question about the atom name, can it be problem if atom
> name start C1......until C1000, or do I need to set the atom name using
> only characters as in amber manual.

Atom names are pretty arbitrary, but can be at most 4 characters long. So,
you can use names like C1 ... C999, but C1000 will not work.

...hope this helps...dac

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Received on Wed Jul 17 2013 - 08:00:02 PDT
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