[Dock-fans] AM1-BCC

Eric Pettersen pett at cgl.ucsf.edu
Thu Oct 5 12:49:45 PDT 2006

> It appears to be an error when I input a ligand (with previously added
> hydrogens) with more than 7 amino acids. See errors above:

Antechamber 1.25 (used by Chimera) has a limit of 128 atoms, which is  
what you are running into.  One option is for you to get Antechamber  
1.27 (which has a limit of 256 atoms) and compile and run it yourself  
using a protonated Mol2 file generated by Chimera.  You would use the  
exact same command that Chimera did (antechamber -i input.mol2 -fi  
mol2 -o output.mol2 -fo
mol2 -c bcc -nc -1 -j 5 -s 2).  You may be able to use the file that  
Antechamber outputs directly in DOCK, or you may have to read it into  
Chimera and have Chimera write a cleaner Mol2 file.

Since your large ligand is composed of a chain of amino acids,  
another option is to edit the structure file you are using as input  
to Chimera and break your DRG residue into the appropriate number of  
amino acid residues (and with appropriate atom names for those  
residues).  Then Chimera will be able to add Amber charges to your  
ligand without invoking Antechamber at all.


                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu

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