[gmx-users] Vacuum Simulation Alanine Dipeptide =>minimisation: ERROR "No default Ryckaert-Bell. types"

Chris Neale chris.neale at utoronto.ca
Fri Aug 22 02:18:58 CEST 2008

 >What do I have to adjust to get rid of the error message?

did you try searching the archives?


-- original message --


to create some toy data I want to do a vacuum simulation of alanine dipeptide with Gromacs.
I used charmm ("generate" command) to build the structure of alanine dipeptide.
The structure in "charmm notation" is  "ACE-ALA-CT3" and in "gromacs notation" is "ACE-ALA-NAC" .
The charmm output is a pdb (in charmm dialect) of alanine dipeptide [see 1].
I looked up the notation in the corresponding OPLS-force field file "/usr/share/gromacs/top/ffoplsaa.rtp" and adjusted it in the pdb file [see 2].
To convert it to a gro file I used following command:

  $pdb2gmx -ter -f alanineDipeptide_gromacsOplsForceField.pdb -p alanineDipeptide_gromacsOplsForceField.top -o alanineDipeptide_gromacsOplsForceField.gro

I selected the "OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)" and 
as a "N-terminus" and a "C-terminus" I selected "None".
The output gro file is [3].

For the energy minimisation I use a sample vaccum script from David van der Spoel from:
  "Gromacs course in 2004 -> Gromacs exercises"

When I run the grompp command I get the error message "No default Ryckaert-Bell" (see [4] for full output):
  $grompp -v -zero -f energyMinimisation_steepSimple.mdp -c alanineDipeptide_gromacsOplsForceField.gro -p alanineDipeptide_gromacsOplsForceField.top -o alanineDipeptide_energyMinimisation.tpr

The corresponding topology file "alanineDipeptide_gromacsOplsForceField.top" is attached.

What do I have to adjust to get rid of the error message?


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