[gmx-users] strange protonate state

[David van der Spoel]

On 2012-11-19 09:57, Albert wrote:
> hello:
>
>    I've got a K+ near an Asp residue. I found that If I include the K+
> in H++ calculation, the Asp is deprotonated while it is protonated if I
> didn't include it. I am quite confused for this. I am just wondering
> will the g_protonate will solve this problem?
>
> thank you very much.
> best
> Albert
This makes sense! The environment is made for a neutral group, which you 
get by either having a K+ or a proton near the Asp.

Normal pdb2gmx will give you the correct topology.

-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se