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

bipin singh bipinelmat at gmail.com
Wed Aug 20 13:11:03 CEST 2014

This might help.


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

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

> 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.  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.
> --
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list