I have a problem minimizing a solvated RNA-hairpin:
With SOLVENT I put 2 shells of water molecules around the hairpin.
VDW-Bump_Factor was set to 0.7.
Dielectric constant was set to a constant value of 1.0, as described in the
Theory Manual (before invoking SOLVENT).
The stem of the hairpin had been defined as an aggregate before using the
Then I invoked MAXIMIN2 (Kollman_All_Atom force field) to minimize the loop.
Electrostatics should be calculated and periodic boundary conditions were
applied (default values).
The Minimizer produced a lengthy list of messages like:
Missing atom types for atom G6.O6
Missing atom types for atom G6.H21
and so on....
The list ended with:
MISSING DATA - Force Field atom type is unknown
What have I done wrong?
Please help me,
Thanks in advance,