[Dock-fans] How to get the charged mol for the ligand

[Eric Pettersen]

I assume this is IMZ from 1rv1?  Chimera is adding a proton to the N3  
nitrogen that it shouldn't.  After adding hydrogens and before saying  
OK to the charge calculation, type this command to Chimera's command  
line to delete the extra hydrogen:

del :IMZ at h3

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu


> I could not get the charges for my molecule (ligand in x-crystal  
> structure). how to do that?
>   I am getting the following error message.
>   I am using chimera to do these funtions.
>
>   Running ANTECHAMBER command: C:\Program Files\Chimera\bin 
> \antechamber\exe\antechamber -i c:\docume~1\thomas\locals~1\temp 
> \tmpkzw4il\ante.in.mol2 -fi mol2 -o c:\docume~1\thomas\locals~1\temp 
> \tmpkzw4il\ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2
> (IMZ)
> (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe 
> \bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC - 
> f ac -j part
> (IMZ)
> (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe 
> \atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
> (IMZ) Total number of electrons: 351; net charge: 1
> (IMZ) INFO: Number of electrons is odd: 351
> (IMZ)       Please check the total charge (-nc flag) and spin  
> multiplicity (-m flag)
> Failure running ANTECHAMBER for residue IMZ
>
>
>   Thomas


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