[gmx-users] Forcefield parameters for Zinc

[Emma A]

Piggot T. <T.Piggot at ...> writes:

> 
> 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 ...
> [gromacs.org_gmx-users-bounces at ...] on behalf
> of Michael Carter [Michael.Carter at ...]
> Sent: 20 August 2014 12:56
> To: gmx-users at ...
> 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 ...> 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 ...>
> >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.
> >>
> >> This e-mail message is confidential and for use by the addressee only.
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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 
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Hi,
Related to the Zn-parameters; where can I find the reference (author, 
journal, year) to the sigma and epsilon (1.95998e-01  5.23000e-02) 
parameters that I find in /gromacs/top/amber99sb.ff/ffnonbonded.itp for [ 
atomtypes ] Zn.

I would like to use amber99sb force field in my Gromacs simulation of a Zn-
containing protein.

Best regards,
Emma 

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