AMBER Archive (2006)

Subject: AMBER: Amber8: problem related to antechamber

From: priya priya (priyaanand_27_at_yahoo.co.in)
Date: Mon Oct 16 2006 - 02:00:38 CDT

 Dear All
 
 When I use antechamber to load a peptoid sequence
 (peptoids have the amino acid side chain appended to
 amide nitrogen ratther then alpha carbon) containing
 charged residues (like lysine). it says "ODD NUMBER OF
 ELECTRONS"....Check!
 
 There are three lysine residues and the total number of electrons come out to be 834 but antechamber is taking 837 number of electrons (not considering the +3 charge of the three lysine residues.
 
 Please suggest how to make the prepin file of such charged residues..
 
 
 
 Sincerely
 Priya Anand
 
                                 
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