[gmx-users] strange protonate state

David van der Spoel spoel at xray.bmc.uu.se
Mon Nov 19 11:22:59 CET 2012

On 2012-11-19 10:42, Albert wrote:
> On 11/19/2012 10:27 AM, David van der Spoel wrote:
>> 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.
> hello David:
>   thanks a lot for such kind reply and comments.
>   Is there any paper concerning on this ion issue? The pdb2gmx make
> correct protonation state of residues in most case, however for some
> special case we probably need more solid evidence to be confirmed. Since
> the protonation state of residue have great impact on later MD productions.
No paper, just basic biochemistry.
In case you suspect an amino-acid should NOT have the default 
protonation you can run pdb2gmx interactively. This is however your 
responsibility as the algorithm is not perfect, in fact it only checks 
the protonation of histidine residues.

> thank you very  much.
> best
> Albert

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

More information about the gromacs.org_gmx-users mailing list