[gmx-users] ACE group in OPLS
urichter at jerini.de
Tue May 17 07:39:55 CEST 2005
I believe Ace is not a standard amino acid defined in the parameter files
you obtain with the Gromacs distribution, at least not for the OPLS-AA
force field. So pdb2gmx might not know how to connect Ace with your
N-terminal residue. I am surprised pdb2gmx did not complain about
the unknown residue. Just check in the topology if there is a bond defined
between the C of Ace and the N-terminus. If not you have to define one
and probably also some other parameters. I have had such surprises
already with other self-defined amino acids.
Robert Hughes wrote:
>The peptide I am simulating is capped at the N-terminus with an acetyl group.
>However, after running pdb2gmx and energy minimization with the OPLS
>forcefield, the ACE group is no longer covalently bound to the N-terminus. I
>have not experienced this same problem with the standard gromacs force field
>(ffgmx). Any ideas on how to get around this?
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