[gmx-users] how to set tolerance for bond formation distance?
feenstra at few.vu.nl
Thu Jun 23 16:28:39 CEST 2005
Kai Zhuang wrote:
> 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
> 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.
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