[gmx-users] system net charge 0f -1.6

Mark Abraham Mark.Abraham at anu.edu.au
Fri Oct 20 03:47:57 CEST 2006

Stefan Schöbel wrote:

> --> why are the HIS residues changed into HISB?

Histidine has different protonation states. You need to choose one of 
them. Apparently, this one is the default. You should apply some 
chemical judgement to ensure you've made a reasonable choice.

> after editconf:
> Generated 279 of the 1225 non-bonded parameter combinations
> Excluding 3 bonded neighbours for Protein 1
> Excluding 2 bonded neighbours for SOL 7683
> Excluding 2 bonded neighbours for SOL 2730
>   System has non-zero total charge: -1.800000e+01
> I tried adding C term Oxygen with spdbv as well, but it still the same uneven charge.

1.8e+01 = 18

> What happened?

You didn't read the computer version of scientific notation properly!


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