VMD-L Mailing List

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Mon Apr 12 2010 - 06:16:42 CDT

On Friday 09 April 2010 09:26:32 Knut Jørgen Bjuland wrote:
> Is it possible to change the the default pH when viewing a protein. I
> would like to see the charge of the protein for pH above 7 ans set it to
> pH 8.5 as an example. Is it also possible to see the amino acid name as
> is possible to do in javamol
>
> Best regards
> Knut j
>

Hi Knut,

You could possibly use H++ (http://biophysics.cs.vt.edu/H++/) to calculate the
protonation stat of the amino acids of your protein. When I remember correctly
it produces a PDB (and other formats) with the amino acids protonated
according to the pH you selected.

Cheers
Bjoern 

-- 
Bjoern Olausson
Martin-Luther-Universität Halle-Wittenberg 
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale
Phone: +49-345-55-24942