[gmx-users] non-integral charge on my modeled protein structure

Mark Abraham Mark.Abraham at anu.edu.au
Sat Apr 10 09:15:20 CEST 2010

On 10/04/2010 5:06 PM, sonali dhindwal wrote:
> Sorry to bother you again but can you please help me in knowing
> "termini",

The ends of polymers often need special treatment. Go and see what 
you've chosen and what makes sense to choose.

> I think total charge (i.e, cumulative) is wriiten at the last
> residue of a protein in [atoms] part of a .top file. that is what i have
> pasted in my previous mail.

Sure, and I pointed out some useful characteristics last time.

> and Mg is in my protein, that is why it is there in topology file. am i
> doing something wrong in that ?

Maybe. Only you know what you're trying to do... If you haven't done it 
right, though, it's one way to end up with non-integral charges.


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