[gmx-users] ACE group in OPLS

Uwe Richter 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.

Uwe

Robert Hughes wrote:

>Hello,
>
>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?
>
>Thanks,
>
>Robert
>
>Robert Hughes
>Graduate Student
>UNC-Chapel Hill
>Department of Chemistry
>B-5 Venable Hall
>Chapel Hill, NC 27599-3290
>(919)-843-6523 (lab)
>(919)-602-1414 (cell)
>(919)-402-0516 (home)
>_______________________________________________
>gmx-users mailing list
>gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please don't post (un)subscribe requests to the list. Use the 
>www interface or send it to gmx-users-request at gromacs.org.
>
>  
>




More information about the gromacs.org_gmx-users mailing list