>What do I have to adjust to get rid of the error message?
did you try searching the archives?
http://www.gromacs.org/pipermail/gmx-users/2006-September/023875.html
http://www.gromacs.org/pipermail/gmx-users/2006-September/023872.html
Chris.
-- original message --
Hi,
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"
https://extras.csc.fi/chem/courses/gmx2004/exercises/index.html
https://extras.csc.fi/chem/courses/gmx2004/exercises/exercise.tgz
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?
Thanks
Emal
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