Subject: Tinker: ionized vs. neutral state

From: "Nicolas Ferre'" <[email-masked]>
Date: Wed, 12 Jun 2002 09:58:15 +0200

Dear CCL,

In Tinker, the charged amino-acids (ASP, GLU and ARG, LYS but not HIS)
are only defined in their ionized state (in the Amber force-field). Is
their an automatic way to protonate the negative residues and to
deprotonate the positive residues ? I still got the corresponding point
charges from the web, however modifying the .xyz file (or the pdb file)
would be a task ... too long !
Or maybe could you point a piece of code that can handle such
manipulations/modifications of a protein structure (possibly free and
not windows-based) ?

Thanks in advance for any help.

Nicolas
-- 
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Nicolas FERRE' (PhD)
				 phone/fax : +39-0577-234278
Dipartimento di Chimica
Universita` di Siena             mailto:[email-masked]
via Aldo Moro
53100 SIENA (Italia)             http://ccmaol1.chim.unisi.it/
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