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

[Michael Carter]

Hi Tom,

Thanks, I will look into it.

I know AMBER has the ZAFF forcefield, and I have done the simulation in AMBER, but I wanted to know if GROMOS forcefields have this capability. I will have a play and see what I can do, most likely I will do a small QM/MM run and use this to parameterise the Zinc ions.

Thanks for the help.

Cheers,
Mike
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Piggot T. [T.Piggot at soton.ac.uk]
Sent: Wednesday, August 20, 2014 4:46 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Forcefield parameters for Zinc and phosphorylated residues

Hi Mike,

As well as the link that Bipin sent, you can also get parameters for GROMOS phosphorylated residues (compatible with the 43A1 force field, I think) from:

http://www.gromacs.org/Downloads/User_contributions/Force_fields

I've never used either so have no idea which might be better. The ones that Binpin suggested look like they work with the newer GROMOS 54A7 force field, so they might be the ones to use.

On your other question, I am not sure about the protein-zinc parameters with a GROMOS force field. I would say, is there any particular need for using one of the GROMOS protein force fields? There are definitely parameters out there for some of the all-atom protein force fields (e.g. AMBER ones) which are probably also better in terms of protein parameters.

Cheers

Tom

PS: Hope things are good in the (relatively) new job!
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Michael Carter [Michael.Carter at icr.ac.uk]
Sent: 20 August 2014 12:56
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Forcefield parameters for Zinc and phosphorylated residues

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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