AMBER Archive (2009)

Subject: [AMBER] some queries on -states flag in constant pH simulation

From: nicholus bhattacharjee (nicholusbhattacharjee_at_gmail.com)
Date: Thu Oct 29 2009 - 23:21:27 CDT

Dear community,
                           The -states flag is used to define the initial
protonated states of the residues. My queries are asfollows

1. Is this flag used only to define protonated states of titratable residues
or all the residues in the protein sequence?

2. Which are the titratable residues?

3. Is it ok to use the default initial protonation states or we have to
specify them? If we have to specify them than how do we know which
protonation states to be specified to which residue? 

-- 
Nicholus Bhattacharjee
PhD Scholar
Department of Chemistry
University of Delhi
Delhi-110007 (INDIA)
Phone: 9873098743(M)
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