AMBER Archive (2006)

Subject: Re: AMBER: constant pH simulation

From: John Mongan (
Date: Tue Mar 21 2006 - 17:51:53 CST

> I have a small problem with the constant pH simulations. I followed the
> instruction in the amber 8.0 user manual, and when I make the cpin file,
> I see a line in the file which says RESNAME='System:Unknown','Residue
> :AS4 376' and so on for all the residues named AS4. Is this something to
> worry about?

No, unless there's some additional problem you haven't mentioned.

You always get "System:Unknown" unless you specify a system with the
-system flag in This is really only useful if you have
experimental pKa values for your titrating groups, and have added this
data to (at the end, see HEWL example). Then you have the option
to select titrating residues by pKa in cpinutil and you get error
calculations when you use calcpka. These data do not affect the
simulation performed by sander in *any* way.


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