Hi
When i say 'the ligand lost its planarity' i mean that the molecule which is a planar aromatic molecule is not planar anymore after the minimization and this is strange.
I'll try to minimaze the ligand itself without the protein and see what appends.
Thank you for the suggestion.
Valentina
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics
Klingelbergstrasse 61 | CH-4056 Basel |
Phone: +41 61 267 15 80
________________________________________
From: David A Case [case.biomaps.rutgers.edu]
Sent: Wednesday, April 23, 2014 7:27 PM
To: AMBER Mailing List
Subject: Re: [AMBER] AMBER minimization problem
On Wed, Apr 23, 2014, Valentina Romano wrote:
>
> I ran an easy and short minimization of the 6-aminopurine-PknG kinase
> complex, but something went wrong.
>
>
> When i saved the pdb file after the minimization, the 6-aminopurine has
> lost is planarity.
Try a minimization of just 6-amino purine by itself; see what you get then.
Saying "lost its planarity" is pretty vague, and you will probably have to
debug this yourself. A ligand could correctly become non-planar when bound to
a protein. Or, antechamber might be underestimating the penalty for non-planar
behavior. Or, (we don't know any of this) you could be visually reacting to a
small amount of non-planarity that is really not important. Or, something
else.
...dac
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Received on Thu Apr 24 2014 - 01:30:04 PDT
