[Dock-fans] amber score regarding cofactor FAD

Scott Brozell sbrozell at rci.rutgers.edu
Wed May 5 19:49:26 PDT 2010


Hi,

On Wed, May 05, 2010 at 01:41:26PM +0800, gongxingwen wrote:
>  
> I am conducting a virtual screening targeting an enzyme containing a cofactor FAD. However, the cofactor FAD cannot be recognized by DOCK6.3 when preparing for amber score. I have resolved this problem using AMBER9 suite. I found a AMBER parameter database at http://www.pharmacy.manchester.ac.uk/bryce/amber#cof. Could these parameters be included in next version of DOCK ? It would be very helpful for docking. 
> Xing-Wen Gong (Ph.D)
> 
> > -----原始邮件-----
> > 主题: [Dock-fans] Announcing: Release of DOCK 6.4

You are a day or two too late to have the parameters in 6.4.
We shall schedule this for 6.5.

You should be able to straightforwardly insert the parameters you have
found into either the user hook library
(dock6/parameters/leap/cmd/leaprc.dock.user)
or the cofactors library (dock6/parameters/leap/cmd/leaprc.dock.cofactors)
since you are an Amber user.
Use one of the existing cofactors, eg, MTX, to find all the details.
There is mention of these libraries here
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AMBERScoreInputs

Scott



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