RE: AMBER: Average PDB - Unusual Bonds

From: Ross Walker <>
Date: Fri, 4 May 2007 08:29:36 -0700

Hi Seth,

As an aside to what Hayden said if you want VMD to preserve the connectivity
- I.e. not recalculate it then you can do the following:

1) Load the prmtop file for this molecule as Amber 7 Parm

2) Load the pdb for this file into the molecule that was just created when
you loaded the prmtop.

In this case VMD will only draw the bonds that are explicitly specified in
the prmtop file.

Note however that you will still likely have very strange bonds. This comes
from the consideration of what an "average structure". It is simply an
average over cartesian space. Consider a methyl group with 3 hydrogens that
is free to rotate - then work out what the average position is of each of
those hydrogens - you will find that they all lie on a single point along
the axis of rotation - incidently a point which none of the hydrogens "ever"
visit during the simulation!

It is often better to consider the most "representative" structure from a
simulation. In this case either the lowest energy structure or a structure
based on cluster analysis. For an overview of this see

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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> -----Original Message-----
> From:
> [] On Behalf Of Hayden Eastwood
> Sent: Friday, May 04, 2007 07:45
> To:
> Subject: RE: AMBER: Average PDB - Unusual Bonds
> Dear Seth
> In my experience an "average" structure is frequently very
> unrepresentative
> of any true molecular state, and the calculation process
> often gives rise to
> bond lengths that differ mearkedly from their normal
> equilibrium values.
> Within VMD a bond is determined by considering the euclidean distance
> between 2 atoms, and if many atoms fall into this Euclidean
> range then many
> bonds are formed and one essentially sees "spaghetti". This
> is a common
> problem of using an "average" structure, I'd suggest that you
> instead find a
> good representative structure, or the lowest, most visited structure.
> I hope that helps
> Hayden eastwood
> Subject: AMBER: Average PDB - Unusual Bonds
> Dear Amber Users,
> I when I use ptraj to create an average stucture of several
> MD or annealing
> runs with a NA structure, the structure has some unusual bond
> connectivity.
> I can load the structure into leap and it looks fine, but in
> VMD and Rasmol
> it looks the same. Has anyone else experienced such behavior?
> Thanks,
> Seth
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Received on Sun May 06 2007 - 06:07:30 PDT
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