Re: [rDock-list-def] Definition of pdb file for waters

[Markus M. <me...@gm...>]

Dear Pascal;
If I understand your question correctly have a look at the manual. There in
chapter 8.3 is the solvent definition section described.
You can define how you would like to treat your waters.
Best,
Markus

On Thu, Nov 7, 2019 at 9:06 AM pascal krezel <pas...@un...>
wrote:

> Hi,
>
> I have some problems with the definition of the pdb file for waters.
>
> If I want all free, how should I write it:
>
> HEADER HYDROLASE
> REMARK 99
> REMARK  99 MOE v2016.08 (Chemical Computing Group Inc.) Thu Nov  7
> 11:38:11 2019
> HETATM    1 OW HOH W   112   50.895   64.748   20.959 1.00 8.00
> HETATM    2 OW HOH W   113   45.384   40.342   22.069 1.00 8.00
> HETATM    3 OW HOH W   114   38.588   39.920    8.942 1.00 8.00
> HETATM    4 OW HOH W   115   41.945   60.472    9.691 1.00 8.00
> HETATM    5 OW HOH W   116   33.544   50.283    1.280 1.00 8.00
> HETATM    6 OW HOH W   117   45.986   60.872    3.752 1.00 8.00
> HETATM    7 OW HOH W   118   45.771   38.003   18.995 1.00 8.00
> END
>
> or
>
> HEADER HYDROLASE
> REMARK 99
> REMARK  99 MOE v2016.08 (Chemical Computing Group Inc.) Thu Nov  7
> 11:38:11 2019
> HETATM    1 OW HOH W   112   50.895   64.748   20.959 8.00 8.00
> HETATM    2 OW HOH W   113   45.384   40.342   22.069 8.00 8.00
> HETATM    3 OW HOH W   114   38.588   39.920    8.942 8.00 8.00
> HETATM    4 OW HOH W   115   41.945   60.472    9.691 8.00 8.00
> HETATM    5 OW HOH W   116   33.544   50.283    1.280 8.00 8.00
> HETATM    6 OW HOH W   117   45.986   60.872    3.752 8.00 8.00
> HETATM    7 OW HOH W   118   45.771   38.003   18.995 8.00 8.00
> END
>
> Sincerely.
>
> Pascal KREZEL
>
>
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