Hi Thomas,
I wounder to know what corrections should I add to the below selection in
case of multi state object
remove solvent beyond 3.5 of polymer
e.g I'm working with the MD trajectory saved in PDB format. I've decided to
deleate all solvent from all 100 frames simultaneously but the above
command works fine only in case of 1 state object .
James
2012/4/26 Thomas Holder <[email protected]>
> Hi Martin & James,
>
> is it just a coincident that you both ask almost the same question?
>
> You could remove all water atoms with few protein contacts or with a small
> surface area. For example:
>
> remove solvent beyond 3.5 of polymer
> set dot_solvent
> get_area solvent, load_b=1
> remove solvent and b > 20
>
> Hope that helps.
>
> Cheers,
> Thomas
>
> On 04/26/2012 10:55 AM, James Starlight wrote:
>
>> Another question- I have my protein.pdb with some inserted crystall
>> waters within protein interiour as well as water surrounded of my
>> protein. I want to remove only sorrounding water but prevent internal
>> water ( wich could be functional relevant ).
>>
>> How I could to select such surrounded water ( e.g via some cutoff
>> radius relative my protein etc) wich I'd like to remove further ?
>>
>
> On 04/25/2012 05:34 PM, Martin Hediger wrote:
>
>> In a crystal structure, there are usually a number of relevant crystal
>> waters, as well as water molecules on the surface. In our approach, we
>> model the protein structure within a dielectric continuum, so surface
>> water molecules are not required (to save computer time). However,
>> waters in the interior should remain in our model. How could we discard
>> the surface waters while keeping the internal waters?
>>
>
> --
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen
>
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