ADL: How to make a flexible chain staying in the active pocket

Gavin Seddon home at gavsed.net
Fri Apr 3 01:53:15 PDT 2009


Jun-Wei wrote:
> Yes. I choose "center on the ligand" and the ligand is placed right in the pocket.
>
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> 2009-04-02?18:07:40,"Gavin?Seddon"?<home at gavsed.net>?:
>   
>> Jun-Wei?wrote:
>>     
>>> ?Dear?AutoDockers,
>>> ??
>>> ?I'm?trying?to?dock?a?ligand?to?a?metalloenzyme?containing?zinc?ion?by?AutoDock4.?The?zinc?is?in?the?active?pocket?of?the?protein.?My?ligand?has?a?sidechain?containing?five?C-C?single?bonds,?which?should?be?located?in?the?active?pocket?theoretically.
>>> ???The?question:?when?checking?the?docking?results,?all?the?docked?poses?bind?to?the?protein?surface?around?the?pocket,?instead?of?binding?into?the?zinc?pocket?with?the?five?C-C?single?bonds.?What?should?I?do?to?get?the?sidechain?into?the?pocket??Thanks?in?advance!
>>> ??
>>> ???The?grid?box?is?properly?set?around?the?pocket?and?different?zinc?parameters?have?been?tried.
>>>
>>> ?Best?wishes,
>>> ?Junwei?Zhao
>>> ?________________________________________________
>>> ?---?ADL:?AutoDock?List??---?http://autodock.scripps.edu/mailing_list?---
>>>
>>> ???
>>>       
>> Have?you?placed?the?gridcenter?inside?pocket?
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>>     
> ________________________________________________
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I had an idea last night. Rather than using a genetic biorhythms for 
dckg, try simulated annealing and pls let me know how you get on since I 
have other interests in sa.


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