[gmx-users] genbox and interatomic distances

[Anton Feenstra]

Markus O Kaukonen wrote:
> 
[..snip..]
> 
> This
> 'Checking Protein-Solvent overlap: tested 0 pairs, removed 0 atoms' looks
> bad.
> 
> And again, water molecules are too close.

If I understand correctly what you are doing, there is no protein,
so no protein-solvent to check. Also, in the terminology of genbox,
there is no solvent. You are generating only 'inserts'...
It could well be that genbox does not check for overlap between
inserted molecules. This option was intended to fill 'holes' in an
existing conformation, where one would only expect overlap between
one inserted molecule and the 'existing' conformation (e.g. protein
and water, possibly with a cavity somewhere). However, I don't feel
like digging through the source to make absolutely sure... :-(
And unfortunately the source is not very easily readable... :-O

But, have you already tried to minimize the generated conformation?
That should quickly remove all these close contacts...


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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