[gmx-users] How to set the charge of zn and cys!

[Maik Goette]

Hi
 > 1. How to set cys deprotonated in Gromacs?

Depends on the forcefield and its entries.
If there is no deprotonated CYS, you can define a new residue without 
proton (RTP,HDB-file).

 > 2. Is charge -0.75 for S in Cys and +1 for zn OK to start with or
 > should i try something else? In that case how to set the charge on the
 > CH2 side group.

Those transition metals are always pain...Maybe, the values aren't that 
bad, because intuitivly, they should keep the zinc fixed in its 
position. It's definitly worth a try...btw. which of the multiple Ryde 
papers are you talking about? Personally, I didn't find the values, yet.
IMHO you shouldn't change antything else than the S-charge on the AA.

 > 3. One could expect that the charge distribution change in cys due to 
 > 1-4 cys coordinated to zinc? If this is the case, how to simulate 
this > or should this effect be ignored.

Hmm...I think, this is as task for the quantum-calculators...in 
classical MD you may ignore that...
Maybe, you could try the new QM/MM-Implemention to simulate one zinc-site.

Regards

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
         mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


Mikko Hellgren wrote:
> Hi all, I would like to get some advice of how to set the charge of a 
> zinc ion non covalent bonded to cys(1,2,3 or 4 cys) in a small peptide 
> 23AA. According to some QM calculation (ref U. Ryde) the cys become 
> deprotonated and have the S atom have an electro-negative charge of -
> 0.75 (4cys-zn) and the zn have a positive charge of about 1, giving a 
> total negative charge of -2 (4*-0.75+1=-2). I have three different 
> questions.
> 
> 1. How to set cys deprotonated in Gromacs? 
> 2. Is charge -0.75 for S in Cys and +1 for zn OK to start with or 
> should i try something else? In that case how to set the charge on the 
> CH2 side group.
> 3. One could expect that the charge distribution change in cys due to 1-
> 4 cys coordinated to zinc? If this is the case, how to simulate this or 
> should this effect be ignored.
> 
> Question number one is probably a very general one, and I think it 
> should be implemented in pdb2gmx (I am not the person to do it 
> though.....)
> 
> Many thanks for all suggestions.
> 
> Mikko Hellgren, PhD student at Karolinska Institutet in Sweden
> mikko.hellgren at ki.se
> 
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