[gmx-users] how to set tolerance for bond formation distance?

[Anton Feenstra]

Uwe Richter wrote:

> Hi,
> 
> 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.

-- 
Groetjes,

Anton

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