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

[Anton Feenstra]

Kai Zhuang wrote:

> 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?

Depends. If you accidentally merged two separate protein chains, it 
probably won't.

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

That's not an error.

-- 
Groetjes,

Anton

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|  _   _  ___,| K. Anton Feenstra                                     |
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