[Dock-fans] sphgen command, generating spheres

Sudipto Mukherjee sudmukh at yahoo.com
Wed Jun 3 09:28:57 PDT 2009


Dear Hannah,

You can create an input file contains answers to all the questions sphgen asks. Then you can run sphgen as:
sphgen -i INSPH -o OUTSPH
where INSPH is a text input file. Here is a sample input file I use:

receptor.ms
R
X
0.0
4.0
1.4
receptor.sph
where receptor.ms is the molecular surface generated. Normally I use the stand-alone dms tool, but the Write DMS tool in chimera works just the same. Sample files from http://ringo.ams.sunysb.edu/index.php/2008_DOCK_tutorial_with_1LAH
Regards
Sudipto Mukherjee
Graduate Student, Robert C. Rizzo Lab
Dept. of Applied Math & Statistics, Stony Brook University



________________________________
From: hannah pamela tan <hpdiamantetan at yahoo.com>
To: dock <dock-fans at docking.org>
Sent: Wednesday, June 3, 2009 4:00:37 AM
Subject: [Dock-fans] sphgen command, generating spheres


Dear Sir,

i'm sorry to ask this question but i really don't have an idea where to apply or execute the sphgen command. i can't fully understand the steps in the dock tutorials. i tried it on the cygwin terminal but it ended up in an error.

i have already installed the dock 6.2 and i have also prepared the ligands and macromolecules to be used (as was instructed in the tutorials).. and i already used the Write DMS tool in the Chimera.

can i please help me on what to do next? thank you!


Hannah Tan
_______________________________________

Smile!  Jesus loves yah!  



      
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