[Chimera-users] Structure editing: add charge

George Tzotzos gtzotzos at me.com
Fri Apr 18 04:28:19 PDT 2014


In relation to my earlier message, I have found a fix (or, at least, I hope I have found one). I have manually edited the ligand.mol file to ensure an integer sum of charges. However, I would welcome any more intelligent way of doing the same.

Apologies for bothering you with this question.

A good weekend to you all

George
 


On Apr 18, 2014, at 8:03 AM, George Tzotzos <gtzotzos at me.com> wrote:

> Hi everybody,
> 
> I’m trying to add  to a ligand intended for an MD simulation using Amber. The ligand is 7-octenoic acid. The charge added to the ligand is non-integer 0.999.
> Given that he unperturbed charge on the protein is +9.000, the charge on the complex is +9.999. Amber does not accept non-integer charges, so it adds on 9 Na+ ions. 
> 
> Is there a way to force the charge on the ligand to be +1.000?
> 
> Apologies if this question should be addressed to the Amber list, but I used chimera to add hydrogens and charges (AM1-BCC). 
> 
> Regards
> 
> George
> 




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