[gmx-users] how to set tolerance for bond formation distance?
feenstra at few.vu.nl
Thu Jun 23 09:55:56 CEST 2005
Uwe Richter wrote:
> it's not quite clear what you mean. Gromacs doesn't look at distances
> to define bonds except for special bonds listed in the file specbond.dat.
> Use chain id's in the pdb file. Otherwise chains will be connected no
> matter what the distances are.
More specifically, pdb2gmx generates topologies from building blocks
with all bonds already defined in them.
Also, pdb2gmx uses the chain ID information in the pdb file to decide
where the polipeptide chain stops.
In addition, some bonds are 'special', like cystein bridges and
covalently bound co-factors like heme. For this the 'specbond.dat'
($GMXDATA/top/specbond.dat) exist. It lists a pair of residue and atom
names and a *required* distance. The bond is created when the actual
distance of the atoms (in your input file) is within 10% of the required
distance. The option -ss will make this interactive, giving you for each
bond the option to have it created or not.
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