[Dock-fans] problem in dms program

shuang luo shuang260 at yahoo.com
Wed Mar 23 13:26:09 PST 2005


Dear Dock users:

I used DMS to create the ms file for the demo receptor rec_fixed.pdb(in the Dock_demo_5.2/ 2_site directory). The problem I encountered is that the ms file dms created is different than the ms file that provided by the demo.

 

Here is the first few lines of rec.ms provided by the demo.

GLY    2    N  18.359   26.869   52.955 A

GLY    2    N  16.822   28.047   53.058 SR0  0.185 -0.437  0.318 -0.841

GLY    2    N  16.967   28.492   53.058 SR0  0.185 -0.541 -0.000 -0.841

GLY    2    N  17.176   28.062   52.797 SR0  0.185 -0.690  0.307 -0.655

GLY    2    N  17.206   27.820   54.986 SR0  0.185 -0.781 -0.608 -0.142

 

Here is the first few lines of ms file generated by the dms program:

GLY    2    N  18.359   26.869   52.955 A

GLY    2    N  16.822   28.047   53.058 SR0  0.185

GLY    2    N  16.967   28.492   53.058 SR0  0.185

GLY    2    N  17.176   28.062   52.797 SR0  0.185

GLY    2    N  17.206   27.820   54.986 SR0  0.185

GLY    2    N  17.331   27.628   54.587 SR0  0.185

 

As you see here, the ms file created by dms miss coordinates of the last three columns.

When I used the ms fle generated by the dms program to run the sphgen, the OUTSPH showed:

density type = X

 reading  newrec.ms                                                                          type   R

 # of atoms =   2316   # of surf pts =  64657

 finding spheres for   newrec.ms                                                                       

 dotlim =     0.000

 radmax =    4.000

 Minimum radius of acceptable spheres?

    1.400000    

 output to  rec.sph                                                                         

 SPHGEN: zero normal for surface point        1

program stops

 

And there is nothing is receptor.sph file. I am a beginner for Dock. Really really appreciated if anyone could give me some hints? Thank you very much.

Best regards

shuang


		
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