[Dock-fans] 答复: Problems with Showbox

zjxu zjxu at mail.shcnc.ac.cn
Tue Dec 16 18:33:43 PST 2008


Hi Carla,

       It seem that there are too many spheres in the cluster 1. In my
opinion, the number of spheres below 100 or 50 is a good choice.

       For dock4, the first two lines are like this:

 DOCK 3.5 receptor_spheres

cluster     1   number of spheres in cluster    35

      If you have modified the .sph file, keep the format like origin.
Sometimes, a white space may cause error.

      Good docking!

 

zjxu

  _____  

发件人: dock-fans-bounces at docking.org [mailto:dock-fans-bounces at docking.org]
代表 00159496 at ufrgs.br
发送时间: 2008年12月16日 星期二 21:05
收件人: dock-fans at docking.org
主题: [Dock-fans] Problems with Showbox

 


Hi,
I'm having some problems with showbox:

showbox < box.in
automatically construct box to enclose spheres [Y/N]?
extra margin to also be enclosed (angstroms)?
   (this will be added in all 6 directions)
sphere file-
cluster number-
fmt: read unexpected character
apparent state: unit 1 named ./selected_spheres.sph
last format: (5X,3F10.5)
lately reading sequential formatted external IO
Abortado

My box.in file have this written:

Y
5
./selected_spheres.sph
1
selected_cluster_box.pdb

And the selected_spheres.sph has this headline:

DOCK spheres within 3.0 ang of ligands
cluster     1   number of spheres in cluster 16592

What should I do to run showbox?

I'm just doing the tutorial, but I want to know how to fix this in case I
get this error again with my protein.

Thank you very much!

Carla

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