[gmx-users] [Fwd: Grompp error (no default RB dihedral)]

David van der Spoel spoel at xray.bmc.uu.se
Fri Jun 10 08:59:31 CEST 2005

On Wed, 2005-06-08 at 07:26 +0200, David wrote:
> -------- Forwarded Message --------
> From: Xiaoming Zhang <xzhang at artsci.wustl.edu>
> Reply-To: xzhang at artsci.wustl.edu
> To: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Grompp error (no default RB dihedral)
> Date: Tue, 7 Jun 2005 17:41:33 -0500 (CDT)
> Dear Dr. Spoel,
> I am a graduate student at Washington University in St. louis.  Currently I am 
> working on the MD simulation in oplsaa ff using GROMACS.  My peptide has 
> an "AIB" residue.  GROMPP complained that the six dihedrals (c-c-c-H) in 
> dimethyl group of AIB are not default RB type.  I was wondering whether it is 
> ok to ignore that warning and how to add parameters for those dihedrals if I 
> want to fix the problem.
edit the AIB entry in ffoplsaa.rtp to add the correct dihedrals. You
will find those in ffoplsabon.itp

If you make it work (and it behaves well) then please report the update
AIB entry back to the list (or to me).
> Thank you very much,
> Xiaoming Zhang
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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