[Dock-fans] GBSA problem with Dock5.2_mac

Suxin Zheng sxzheng at u.washington.edu
Fri Jul 8 11:39:13 PDT 2005


Hi,

I am using the pre-compiled dock5.2 for mac. I have run the demo test  
with no GBSA term which is OK. Then I try to use the GBSA score.  
First, I build INCHEM for gb and use nchemgrid_GB to generate the  
gb_grid. Second build another INCHEN for sa and use nchemgrid_SA to  
generate the sa_grid. Then I rebuild the dock.in file for gbsa score  
as the attachment. (I found it need to change the gbsa_score_primary  
to gbsa_pairwise_score_primary, is it right. I have recompile the  
sphgen and grid program.)
Then I use: dock5 -i gbsa_dock.in -o gbsa_dock.out
it gives out: Bus error when reading the nrg grid.

the grid.in, gbsa_dock.in and gbsa_dock.out are enclosed.

Could somebody deal with this problem.

Thank you
suxin
-------------- next part --------------
A non-text attachment was scrubbed...
Name: INCHEM.gb
Type: application/octet-stream
Size: 947 bytes
Desc: not available
Url : http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20050708/c723e377/INCHEM.obj
-------------- next part --------------
A non-text attachment was scrubbed...
Name: INCHEM
Type: application/octet-stream
Size: 655 bytes
Desc: not available
Url : http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20050708/c723e377/INCHEM-0001.obj
-------------- next part --------------
A non-text attachment was scrubbed...
Name: gbsa_dock.in
Type: application/octet-stream
Size: 4582 bytes
Desc: not available
Url : http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20050708/c723e377/gbsa_dock.obj
-------------- next part --------------
A non-text attachment was scrubbed...
Name: gbsa_dock.out
Type: application/octet-stream
Size: 6392 bytes
Desc: not available
Url : http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20050708/c723e377/gbsa_dock-0001.obj
-------------- next part --------------
A non-text attachment was scrubbed...
Name: grid.in
Type: application/octet-stream
Size: 709 bytes
Desc: not available
Url : http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20050708/c723e377/grid.obj
-------------- next part --------------
A non-text attachment was scrubbed...
Name: grid.out
Type: application/octet-stream
Size: 6704 bytes
Desc: not available
Url : http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20050708/c723e377/grid-0001.obj
-------------- next part --------------
A non-text attachment was scrubbed...
Name: dock.out
Type: application/octet-stream
Size: 5564 bytes
Desc: not available
Url : http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20050708/c723e377/dock.obj
-------------- next part --------------
----------------------------------------------------------------------
Suxin Zheng
Box 351700
Department of Chemistry, University of Washington
Seattle, WA, 98195-1700
sxzheng at u.washington.edu





More information about the Dock-fans mailing list