[gmx-users] Forcefield parameters for Zinc and phosphorylated residues

[bipin singh]

This might help.

http://vienna-ptm.univie.ac.at/



*------------------------Thanks and Regards,Bipin Singh*



On Wed, Aug 20, 2014 at 4:30 PM, Michael Carter <Michael.Carter at icr.ac.uk>
wrote:

> Hi,
>
> I have two questions regarding the parameterisation of Zinc ions and a
> phosphorylated TYR residue within two different protein systems.
>
>
>  1.  Zinc parameters:
>
> I have three zinc ions within one protein system. I want to use a bonded
> model so that they do not fly out of my protein upon simulation. Is there
> any documentation on the parameters for such a model in the GROMOS
> forcefield?
>
> 2. Phosphorylated TYR
>
> In another system I have a phosphorylated TYR residue. PDB2GMX does not
> like this and after looking inot the manual I have found that you can add
> parameters for this to the existing forcefields. Much like the previous
> question, is there any documentation on the addition of parameters for
> phosphorylated residues in the GROMOS forcefield?
>
> Any pointers for these questions would be greatly appreciated.
>
> Cheers,
> Mike Carter
>
> The Institute of Cancer Research: Royal Cancer Hospital, a charitable
> Company Limited by Guarantee, Registered in England under Company No.
> 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.
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