[AMBER] charged or not

From: s. Bill <s_bill36.yahoo.co.uk>
Date: Thu, 9 Jul 2009 13:33:05 +0100

I am new AMBER user and  I am working on simulating a carboxylate ligand with a protein.
During defining the carboxylate ligand as a non-standard residue (using Antechamber), I defiend it as carboxlic acid (where there is no atom type for the charged oxygen), is this right?
but, now when I loaded my pdb file, xleap will add hydrogen, subsequently, it will add hydrogen to the my ligand's oxygen.
Ok, in this case, should I delete this hydrogen atom on oxygen or do what? my work should run on carboxylate not carboxylic?
Thanks in advance
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Received on Thu Jul 09 2009 - 10:08:54 PDT
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