[gmx-users] Modeling Zinc in OPLS

[Maik Goette]

Hi

Thats fine. The zinc in my structure is also stabilizing the 
strucutre...possibly, you are working on zinc finger ? ;)

What I did, was reading a few papers about that zinc stuff, and what I 
found out was the following for the bonded approach:

Bonded approach seems ok for any zinc, that are NOT catalytically active.
The charge of bonded zinc is set somewhere around 0.7. A charge of 2 was 
mentioned to be not realistic.
Second thing is, as you mentioned, the charges of the complexing atoms.
First, one should intuitivly deprotonate the CYS sulfur. Second, the 
complexing nitrogen of HIS has to be deprotonated. If the HIS overall is 
neutral or deprotonated at the other nitrogen, too (and therefore a 
histidinate) is not clear to me yet. I personally think, that depends on 
your system and the HIS neighbours. I used a neutral HIS and it worked 
fine for me (as other also did).

What I did, was taking the charge of the zinc, divided it by the number 
of complex partners, and added the "quarter-charges" to the complexing 
AAs, to get a neutral system overall. Therefore, the sulfur in the CYS 
got the whole "quarter-charge", and the partial charge for the 
histidines was equally divided onto the heavy atoms of HIS (just those 
in the ring).

Angles and bond-lenghts can be measured from the structure. Feel free to 
set up your own force constants. I did that intuitively and it seems to 
work fine.

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/


Sandeep Somani wrote:
> Hi Maik
> 
> In my protein the Zn is bonded to 3 CYS and a HIS and is stabilising the
> local structure. 
> 
> So ill also have to use the bonded approach which means there will be
> change in parameters for the surrounding CYS and HIS too (?). 
> 
> waiting for more details from you .. 
> 
> thnx & rgds
> sandeep
>  
> 
> 
>>-----Original Message-----
>>From: gmx-users-bounces at gromacs.org 
>>[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Maik Goette
>>Sent: Wednesday, March 02, 2005 4:43 PM
>>To: Discussion list for GROMACS users
>>Subject: Re: [gmx-users] Modeling Zinc in OPLS
>>
>>
>>Hi
>>
>>I also use Zn in my simulations.
>>There are 3 possibilities:
>>Bonded, nonbonded and cationic dummy atom approach. 
>>Unfortunatly, nothing except the bonded approach worked for 
>>me. If you need help with the bonded approach, tell me. If 
>>you are able to work with one of the both nonbonded methods, 
>>tell me. What is the job of zinc in your sim?
>>
>>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/
>>
>>
>>Sandeep Somani wrote:
>>
>>>Hi
>>>
>>>I have a Zn atom in my protein cordinating with CYS and HIS.
>>>
>>>Is it fine to model it with just the non-covalent 
>>
>>interactions (using 
>>
>>>parameters available in the OPLS force filed) or a bonded 
>>
>>interaction 
>>
>>>should be considered ?
>>>
>>>Thnx & Rgds
>>>Sandeep
>>>
>>>---
>>>Research Associate
>>>Computational Biology Group
>>>Bioinformatics Institute
>>>Singapore
>>>
>>>---
>>>Outgoing mail is certified Virus Free.
>>>Checked by AVG anti-virus system (http://www.grisoft.com).
>>>Version: 6.0.859 / Virus Database: 585 - Release Date: 2/14/2005
>>> 
>>>
>>>_______________________________________________
>>>gmx-users mailing list
>>>gmx-users at gromacs.org 
>>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>>Please don't post (un)subscribe requests to the list. Use the
>>>www interface or send it to gmx-users-request at gromacs.org.
>>>
>>>.
>>>
>>
>>_______________________________________________
>>gmx-users mailing list
>>gmx-users at gromacs.org 
>>http://www.gromacs.org/mailman/listinfo/gmx-> users
>>Please 
>>don't post (un)subscribe requests to the list. Use the 
>>www interface or send it to gmx-users-request at gromacs.org.
>>
>>---
>>Incoming mail is certified Virus Free.
>>Checked by AVG anti-virus system (http://www.grisoft.com).
>>Version: 6.0.859 / Virus Database: 585 - Release Date: 2/14/2005
>> 
>>
> 
> 
> ---
> Outgoing mail is certified Virus Free.
> Checked by AVG anti-virus system (http://www.grisoft.com).
> Version: 6.0.859 / Virus Database: 585 - Release Date: 2/14/2005
>  
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> 
> .
>