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

[Michael Carter]

Hi Bipin,

Thanks for this. It works well for adding functionality to residues.

Cheers,
Mike Carter


On 20/08/2014 12:10, "bipin singh" <bipinelmat at gmail.com> wrote:

>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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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.

This e-mail message is confidential and for use by the addressee only.  If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.