[gmx-users] Is there C=C in ffgmx.atp?

[Anton Feenstra]

Markus O Kaukonen wrote:
> Dear All,
> 
> I'd like to use Gromacs with all hydrogens included.
> This is done by choosing option
> 
>>1: Gromacs Forcefield with all hydrogens (proteins only)
> 
> in 'pdb2gmx'
> 
> Question:
> How are the C=C double bonds defined for aliphatic hydrocarbons
> with this force field?
> (I was unable to find a proper atom type in ffgmx.atp)

The double bond comes from the (improper) dihedral, not necessarily
from the atom types. Check, e.g., the N-C peptide bond.

N.B. the ffgmx2 forcefield is old, I wouldn't use it. IIRC, the OPLS
ff's are also all-atom.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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