AMBER Archive (2009)

Subject: [AMBER] charged or not

From: s. Bill (s_bill36_at_yahoo.co.uk)
Date: Thu Jul 09 2009 - 07:33:05 CDT

Dear AMBER
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
Bill

      
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber