[AMBER] distrbuting an excess charge

From: Homa Azizian <homa.azizian.anu.edu.au>
Date: Mon, 12 Apr 2010 15:50:30 +1000

I am new user of amber. I want to creat library file for carbamylated-lysin (as non-standard residue) wih total charge of -1. At the final stage, after I constructed it with xleap, I must omit two hydrogens: one from H-C=O and the other from H-N-H peptide bond, As the other standard residues don't have them. The residue's charge changes from -1 to -1.396250. So I must distribiute the 0.396250 excess charge to C and N. But I dont know how to add these chages (with which proportion) to C and N.
Any suggestion would be appreciated.
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Received on Sun Apr 11 2010 - 23:00:03 PDT
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