[Dock-fans] Amber charges and GB/SA docking

Terry Lang terry at cgl.ucsf.edu
Thu Feb 24 19:28:17 PST 2005

>1) It states in the Dock4 manual (page 22) that you should use
>KOLLMAN all-atom
>charges in Sybyl when constructing the grid. In my Sybyl6.9, these
>charges are not the
>same as the best-known Cornell et al Amber94 charges, which you can
>get from Sybyl by
>using the Amber95dna dictionary. I'm thinking that I should go with
>Amber94, but what are the
>bulk of published works with DOCK based on, or the opinions of
>current DOCK experts?

The majority of the work from the Kuntz lab has been done with the Amber94 
charge model.  We are currently comparing a variety of charge models for 
RNA, but we do not have any solid conclusions yet.

>2) I've referred a lot to a paper by Kang et al (Biopolymers 73, pg
>192), which used the GB/SA
>scoring function to rank minor-groove binding ligands, with
>reasonable success.
>My initial, very preliminary, runs (on a Zinc database) seems to rank
>ligands 'better' with the
>plain dock energy function. By 'better' I mean molecules which lie
>substantially inside the groove
>are ranked higher than those only partially attached to the DNA.
>I know many things might be happening, but specifically I'd like to
>try using the refit GB/SA
>scoring functions of the above paper (Table II). Can someone tell me
>how to modify the Dock code
>to do this? Line  621  in score_d4.cpp seems apposite, but I don't
>quite understand the relation
>between these variables and the equations as written in the paper.

I would recommend contacting Dick Schafer (author to contact with 
questions) and ask him how they went about it.  We do not include these 
parameters in our distribution of DOCK and do not currently have plans to 
include it in the future.

>Thanks for your attention,
>Dock-fans mailing list
>Dock-fans at docking.org

***NOTE:  This is a new e-mail address (terry at cgl.ucsf.edu)  Please update 
your address book!***

P. Therese (Downing) Lang
Kuntz and James Labs
UCSF - CCB Graduate Program
Phone:  (415)476-3986

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