From: Floris Buelens (floris_buelens_at_yahoo.com)
Date: Mon Sep 10 2007 - 09:50:46 CDT
This web service, PDB2PQR, is excellent:
http://agave.wustl.edu/pdb2pqr/server.html
It includes the option to assign protonation states using PROPKA (as Peter suggested) for an uploaded pdb file.
Best of luck
Floris Buelens
Department of Crystallography, Birkbeck College, London
----- Original Message ----
From: "Wang, Boyang" <bwang9_at_uic.edu>
To: namd-l_at_ks.uiuc.edu
Sent: Monday, 10 September, 2007 1:47:33 AM
Subject: namd-l: The charged states of histidines in green fluorescent protein.
Dear all,
green fluorescent protein, (for example, PDB ID 1W7S) has about 10
histidines. I wonder how I could get the charged states (positively
charged or neutral) of each histidine.
One way to do it is to try different charged states and study the
stability of the protein, which actually takes a long time.
Thanks a lot for your considerations!
Boyang.
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