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Gerber Molecular Design |
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- Accepts united-atom or explicit hydrogen structures
- Automatic recognition of molecular topology from heavy atom H-counts
- Automatic parameter assignment
- Handling of conjugated systems
- Intramolecular interaction terms extensively tested against small molecule X-ray data
- Strictly finite range interaction terms
- No atomic charge values needed
- Geometric H-bond terms for polar non-bonding interactions
- H-bond strength-value assignments based on hydration data
- H-bond pattern evaluation
- Wide variety of constraining terms
- All energy terms separately weighable
- Langevin type dynamics

- C-alpha positions and phi-psi values as variables
- Bonded interaction terms to maintain correct peptide geometry
- Geometrical H-bond terms for peptide-peptide interactions
- Known secondary structures as energy minima
- Strictly finite range interaction terms
- Wide variety of constraining terms
- Langevin type dynamics

- MAB parametrization can be transferred to files readable by GROMOS or X-PLOR.
- Explicit hydrogens can be attached in positions according to a MAB-calculated H-bond pattern.