AMBER Archive (2008)

Subject: Re: AMBER: Querry about simulating a glycopeptide

From: Lachele Foley (Lists) (
Date: Tue Aug 12 2008 - 09:03:14 CDT

It is unlikely that the bond was broken. It is more likely that the
bond between the carbohydrate and the protein was never set (or never
set properly) in the first place. With some viewers, bonds can appear
to be present, but they might not be recognized by Amber programs.
For example, when using VMD to view the complex based on a pdb file,
VMD will typically bond by distance, and it will appear that a bond
exists. However, unless the bond is explicitly set in the prmtop
file, Amber will see those atoms as merely being close to each other.
To test your situation, try loading the initial AMBER prmtop and
coordinate files used for your simulation (rather than the pdb) into
VMD. If there isn't a bond, then you need to add one. The AmberTools
manual contains an example describing a method for doing this starting
from a pdb file.

On Tue, Aug 12, 2008 at 6:23 AM, dipti lele <> wrote:
> Hello everyone.
> As per your help now I could get the parameter files for the carbohydrate
> moiety for my glycopeptide. When I minimised the energy and went for the
> simulation. The bond between thr and the carbohydrate moiety is found to be
> broken. Why is this happening? I did not get it. Do I need to use any
> constraint?
> --
> Deepti Lele,
> NII, New Delhi.

:-) Lachele
Lachele Foley
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