[gmx-users] strange protonate state

Albert mailmd2011 at gmail.com
Mon Nov 19 10:42:20 CET 2012

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.

thank you very  much.

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