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

Michael Carter Michael.Carter at icr.ac.uk
Wed Aug 20 13:01:11 CEST 2014


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.

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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