[Chimera-users] any aid for dock3.5 score?

Francesco Pietra chiendarret at gmail.com
Sat May 9 00:47:15 PDT 2009

Hi Elaine:
Do you know if standard capping groups (ACE NME) pose special
problems, or are you aware if there is a charge assignment for them in
relation to delphi? At any event, should their charge be adjusted so
that the total charge of the protein is unitary?

As the chimera tool is old, any idea if it faces problems with current
version 4 of delphi?

Any plan to make use of apbs in this context?


On Thu, May 7, 2009 at 2:20 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Francesco,
> If by "the grid" you mean the potential map from DelPhi:
> If you have the academic version of DelPhi from the Honig Lab, you can run
> it with the Chimera tool DelPhiController (under Tools... Surface/Binding
> Analysis):
> <http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/delphicontroller/delphicontroller.html>
> This allows entering all the DelPhi run parameters and input/output
> filenames into a GUI instead of the text files needed to run DelPhi
> "manually."  However, it does not help you make sure parameters are
> correctly assigned; you are still responsible for figuring out which DelPhi
> charge and radius files (also from the Honig lab) to use and making sure the
> atoms in your structure are named correctly to match with the parameters in
> these files.
> Also, DelPhiController is one of our older tools and may not be very easy to
> use.
> Elaine
> -----
> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                      http://www.cgl.ucsf.edu/home/meng/index.html
> On May 6, 2009, at 10:14 AM, Francesco Pietra wrote:
>> Hi:
>> I am considering to use dock3.5 score in DOCK6.2, which makes use of
>> Delphi. Is any aid in chimera for builing the grid?
>> thanks
>> francesco

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