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

Jun-Wei zhaojunwei2004 at 126.com
Fri Apr 3 01:10:45 PDT 2009


Yes. I choose "center on the ligand" and the ligand is placed right in the pocket.




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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