Subject: Autodock3.0 gpf parameter problem.

From: Keun Woo Lee <[email-masked]>
Date: Thu, 10 Feb 2000 16:18:38 -0600

Hello,

I am currently using AUTODOCK3.0 but recently I found there are two
parameters
for GPF file (i.e. for making GRID map files) as the followings:

<For example for Carbon atom>
Case 1.
----------------------------------------------
map  protein.C.map #filename of grid map
nbp_r_eps 4.00 0.0222750 12 6 #C-C lj
nbp_r_eps 3.75 0.0230026 12 6 #C-N lj
nbp_r_eps 3.60 0.0257202 12 6 #C-O lj
nbp_r_eps 4.00 0.0257202 12 6 #C-S lj
nbp_r_eps 3.00 0.0081378 12 6 #C-H lj
nbp_r_eps 3.00 0.0081378 12 6 #C-H lj
nbp_r_eps 3.00 0.0081378 12 6 #C-H lj
sol_par 12.77 0.6844
constant 0.000
-----------------------------------------------

Case 2.
-----------------------------------------------
map protein.C.map           #atomic_affinity_map
nbp_r_eps  4.00 0.1500  12   6  #C-C non-bond Rij & epsilonij
nbp_r_eps  3.75 0.1549  12   6  #C-N non-bond Rij & epsilonij
nbp_r_eps  3.60 0.1732  12   6  #C-O non-bond Rij & epsilonij
nbp_r_eps  4.00 0.1732  12   6  #C-S non-bond Rij & epsilonij
nbp_r_eps  3.00 0.0548  12   6  #C-H non-bond Rij & epsilonij
nbp_r_eps  3.00 0.0548  12   6  #C-H non-bond Rij & epsilonij
nbp_r_eps  3.00 0.0548  12   6  #C-H non-bond Rij & epsilonij
---------------------------------------------

In the Autodock homepage in Schripps (
http://www.scripps.edu/pub/olson-web/doc/autodock/), the Case2 is
listed in the parameter page. But in FAQ page, the Case 1 parameter
is listed. In AUTODOCK3.0 manual, the Case2 parameter was used
in the example xxx.gpf file in appendix.

In the results of the calculation for both,  the Docking energy of Case2
is
lower than Case1 by about seven times.

Which one is right ? Can you someone give me the answer or some clue
about this ?

Thank you in advance.

Kunu

==============================================
    Keun Woo Lee,  Ph.D.
    Postdoctoral Associate
    Department of Biology and Biochemistry
    University of Houston
    Houston, TX 77204-5513
    Phone: (713) 743-8389, 8367
    Fax:   (713) 743-8351
    Email:  [email-masked]
    http://adrik.bchs.uh.edu/~kwlee
==============================================