AMBER Archive (2006)

Subject: AMBER: peptide simulation before docking

From: jitrayut jitonnom (jitrayut.018_at_gmail.com)
Date: Sat Jul 08 2006 - 15:45:28 CDT

Dear everybody,

Actually, I am new for peptide docking and I have problems about docking
peptide ligand (heptapeptide) to enzyme receptor (trypsin) by Autodock 3. To
screening and finding the binding mode of 24 heptapeptides with autodock,
it will take much cpu time to run according to blind docking (Hetenyi &
Spoel et al). So, my questions is clasified in two cases;
(1) For, heptapeptides ( no x-ray structure). How can I obtain the
conformation of these peptides before docking? Actually, i have already done
by AM1 semiempirical (Spartan '04) but I am not sure this is right because
some papers use MD simulation ,but, did not tell much details (simulation
time, implicit or explicit) on simulation, so I want some suggestions from
anyone about setting the system for peptide simulation like this case.
(2) For docking, I want to know that " Is there another way to screen this
peptide complex by autodock",? Maybe can i reduce parameters such as
ga_pop_size ,ga_num_eval, or ga_run for this system. Which are the
appropriate parameters for the fast screening in this case?

Thank in advance,

Jitrayut Jitonnom, Ph.D.(candidate)
Dept. of Chemistry,
Computational Simulation,
and Modeling Laboratory (CSML),
Chiang Mai University, Thailand.
Tel: +66(0)6613-4218
Email: jitrayut.018_at_gmail.com <shafinaz_at_bri.nrc.ca>

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