AMBER Archive (2006)

Subject: AMBER: Fwd: ADL: peptide simulation before docking

From: jitrayut jitonnom (jitrayut.018_at_gmail.com)
Date: Sun Jul 09 2006 - 04:26:59 CDT

Hi everyone,

I think that autodock usually do when the ligand and enzyme from x-ray, but
sometimes ligands and enzyme can be created and optimized prior to
docking. Most ligand will be optimized by gaussian or other program
to obtain the structure and charge. But I was wondering in case of
heptapeptide should I do optimize by gaussian or other quantum program, or
should I do the md simulation by protein force field program like amber
,etc.

Can anyone explain this problem ? so I will thanks a lot.

Jitrayut

---------- Forwarded message ----------
From: Paul Wilhelm Elsinghorst <paul_at_uni-bonn.de>
Date: 9 ¡.¤. 2006, 15:18 ¹.
Subject: Re: ADL: peptide simulation before docking
To: jitrayut jitonnom <jitrayut.018_at_gmail.com>

Hi guys,

I pick up this question for I had similar thoughts. Using GA docking I
was wondering if I would need energy minimization at all prior to
docking. Why not just take a the stretched molecule (small ligand,
heptapeptide, etc.) and dock it. Gas phase energy minimization should
not give results close to the enzyme binding mode and thus won't speed
up the docking process.

What do You think?

Paul
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu