ADL: problem with .SA.map

Bernhard Knapp bernhard.knapp at meduniwien.ac.at
Thu Jan 24 00:31:40 PST 2008


Dear John

I had/have a similar problem, see mail-stack: ADL: can't find or open  
*.receptor.C.map
By the way decribed below i could start autodock, but i dont think the 
results will be correct.
If you find a better way of solving that problem please tell me.

- Bernhard





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is it possible that there is a problem in the prepare_gpf4.py script? 
because i restartet it a few times with ligand_types="X", where X is 
always an other needed type. by this way i could create all the 
necessary complexLLFGAPVYV.receptor.X.map files and start autodock. if i 
set ligand_types to "A C H OA N S" i does not work. but the problem in 
this solution is that autodock thinks that only one atom type is 
existing in the ligand (written to the *.gpf file, which is created 
without seg fault) this may lead to wrong docking results ...

is there a way of simply using the autodock scoring function as 
described in (Huey et al., 2007) on a given fixed receptor/ligand 
conformation (without any screening of spatial space or ligand flexibility)?


cheers

Bernhard

 


Huey,R., Morris,G.M., Olson,A.J., and Goodsell,D.S. (2007). A 
semiempirical free energy force field with charge-based desolvation. J 
Comput Chem. 28, 1145-1152.

 





Sargis Dallakyan wrote:


>>>>if I simply add 
>>>>"map hsg1.SA.map"
>>>>to the gpf file it says "ERROR: Too many "map" keywords (2); the "types" 
>>>>command declares only 1 maps."
>>>>
>>>>if i change the map line to "map hsg1.SA.map" it complains with
>>>>"I'm sorry; I can't find or open  "complexLLFGAPVYV.receptor.C.map"
>>>>    
>>>>
>>    
>>
>>
>>Sorry for the confusion. "map hsg1.SA.map" should be added if you add a ligand 
>>type explicitly to .gpf file. I was thinking that your problem is similar to 
>>Monica's problem when I posted and hsg1 is an example used for debugging.
>>
>>  
>>
>  
>
>>>>also if i remove the SA from  the "-p ligand_types="A C Cl H F OA N P S 
>>>>Br NA SA HD"" it does not help and it still says "I cant find or open 
>>>>"complexLLFGAPVYV.receptor.N.map""
>>>>
>>>>what am I doing wrong?
>>>>    
>>>>
>>    
>>
>>
>>In your case, something else is causing a problem, since you used 
>>prepare_gpf4.py which adds "map *.*.map" lines automatically.
>>
>>  
>>
>  
>
>>>>>>>>/home/bknapp/MGLTools-1.4.6/share/bin/pythonsh 
>>>>>>>>/home/bknapp/MGLTools-1.4.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_gpf4.py 
>>>>>>>>-o complexLLFGAPVYV.gpf -l complexLLFGAPVYV.ligand.pdbqt -r 
>>>>>>>>complexLLFGAPVYV.receptor.pdbqt -p ligand_types="A C Cl H F OA N P S Br 
>>>>>>>>NA SA HD" -p gridcenter="grid center coordinates" -p npts="grid points"
>>>>>>>>        
>>>>>>>>
>>>>        
>>>>
>>
>>Instead of "grid center coordinates" and "grid points" use ADT or similar tool 
>>to find numeric values for these parameters (e.g. npts="60 60 60"). You can use 
>>'auto' for gridcenter in which case autogrid will use the center of the 
>>macromolecule.
>>
>>There is recent thread about a bug in prepare_gpf4.py. If you type 
>>gridcenter="2.5 6.5 -7.5" you might end up with
>>gridcenter 2.5                      # xyz-coordinates or auto
>>in your .gpf instead of
>>gridcenter 2.5 6.5 -7.5             # xyz-coordinates or auto
>>
>>Add the missing numbers with a text editor if this is the case.
>>
>>  
>>
>  
>
>>>>>>>>/home/bknapp/downloads/autoDock_4/i86Linux2/autogrid4 -p 
>>>>>>>>complexLLFGAPVYV.gpf -l complexLLFGAPVYV.glg
>>>>>>>>        
>>>>>>>>
>>>>        
>>>>
>>
>>Do you get segmentation fault after this step? If not, type
>>more complexLLFGAPVYV.gpf
>>or run autogrid4 without "-l complexLLFGAPVYV.glg" to monitor the progress.
>>
>>-Sargis
>>________________________________________________
>>--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>>
>>
>>  
>>
>  
>


________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---




 






John Bruning wrote:

>Hi,
>
>I am new to Autodock. I went through the tutorial with no problem, then I
>tried my own protein...
>
>When I try to launch Autodock4 thru ADT it terminates and apologizes to me
>that it cannot find my .SA.map file. The file apparently doesn't exist
>because Autogrid did not create it;  but Autogrid doesn't complain to me
>that it is not making the file and seems to run fine.  The only error I get
>thru the whole process is in the setting up of the grid making (just prior
>to running Autogrid) and a complaint that I have some amino acids with
>partial charges that need to be fixed.  The error doesn't tell me how to
>fix.  I guess there may be something wrong with my pdb.  Any ideas why
>Autogrid is not making all the appropriate maps?
>
>
>Thanks,
>John
>________________________________________________
>--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
>
>  
>



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