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

[Kai Zhuang]

thx.

i actually found out i made a mistake.
it turns out that atom number shown by pdb2gmx is the atom number in
the .gro file produced,
not in the .pdb input file.  (i didn't know that, i thought the atom
numbers are the same)

so now i just basically have two long bonds with high energy, between
two backbond carbons.

would minimization solve this problem?

i tried to minimize them but i got the "reach machine precision but
not converge to the requisigh red FMax" error after 140 steps.




On 6/23/05, Anton Feenstra <feenstra at few.vu.nl> wrote:
> 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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> |  _   _  ___,| K. Anton Feenstra                                     |
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-- 
Kai Zhuang
BioMedical Engineering @ University of Toronto
kai dot zhuang at gmail dot com
kai.zhuang at gmail.com
6478314789