[Dock-fans] about autoDMS

GK Show gkxiao at yahoo.com.cn
Thu Apr 10 00:23:19 PDT 2008


I have compile a binary dms for Cygwin under MicroSoft Windows.
Please download:http://www.shufaxuexi.com/dms.tar.bz2
And I have write a autoDMS to run the dms.
How to install:
1)Make sure you have install python for you Cygwin
2)Put the dms.tar.bz2 in the /usr/
3)cd /usr/
4)bunzip2 dms.tar.bz2
5) tar -vxf dms.tar
How to use:
1)remove the water ,ion, ligand and other HETATM from your receptor,and save it as a PDB file.
SPDBV will help you to do it.
For example: receptor.pdb
2)extract the ligand from complex and save it as a PDB file.
SPDBV will help you to do it.
For example: receptor.pdb
3)extract the pocket residues which is the amio acids within a specified radius,ie. 7A. around the lignad,and save it as a PDB file.
you need to save it as near.pdb
4)I have write a python script, condense.py, which will generate a amino acid list.
   And autoDMS will call dms with -a flag to generate a surface only for the pocket.
   Now make sure you put the files receptor.pdb and near.pdb in the same directory.
   You just type the command in that directory:
   autoDMS  
   a prompt will appear like following:
  
Usage: autoDMS <receptor_pdbfile> [<surface_density>] [<probe_size>]
    where <surface_density> defaults to 5.0 and probe size to 1.4.
    For example: autoDMS dfr.pdb 3 1.45)You can type:
autoDMS receptor.pdb  3 1.4
you can get the file: receptor.ms INSPH
That is it.
Here is the condense.py which released as a Fortran program in dock5.
----------------->code begin here<--------------------
# a script to create amino acid listed  used for DMS
# USAGE:
# STEP1: select active site residues with spdbv and save it as near.pdb
# STEP2: run this python script file,just type:
# python condense.py >> aalist
# or just type:
# python condense.py
# condense will list the amino acid resudes of the near.pdb
# This aalist file will be used in DMS as temple file
# USAGE:
# dms pdbfile.pdb -a -n -d 5 -i aalist -o pdbfile.ms
f=open('near.pdb')
lines=f.readlines()
f.close()
for eachLine in lines:
    if eachLine[0:4]=='ATOM' or eachLine[0:6]=='HETATM': 
       print eachLine[17:20],eachLine[23:26]+'%s' % eachLine[21:22],eachLine[12:16]
------------------------->code end here<-----------------------------------------------

you just save it as condense.py, that is OK!

Happy docking!
PS:
DMS only work for a unix file format!!!!

solomon xiao
gkxiao at yahoo.com.cn



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