Re: [gmx-users] tyrosyl radical force field

Thanks Tsjerk, In my system, I need to model one of the TYR side chains in radical form. Now while doing that I need to get proper charges as you said. According I have calculated the ESP charges in Gaussian for the TYR radical [ unprotonated,neutral, terminals are capped with -NMe and -COCH3] . No

Re: [gmx-users] tyrosyl radical force field

It's a radical approach, for certain! But do mind that the tyrosyl side chain is a conjugated system, so the charge goes all over the place, and you have to do (proper) QM calculations to see where it ends up. Radical approaches are not suitable for radical parameters :p Tsjerk On Wed, Oct 3, 201

Re: [gmx-users] tyrosyl radical force field

On 10/3/12 7:49 AM, tarak karmakar wrote: Thanks Justin, Actually if I would remove the proton from the tyrosine -OH and add the corresponding charge of the Hydrogen to the phenolic oxygen to keep the residue neutral then wouldn't it be convenient to think as if it's a radical ? That doesn't

Re: [gmx-users] tyrosyl radical force field

Thanks Justin, Actually if I would remove the proton from the tyrosine -OH and add the corresponding charge of the Hydrogen to the phenolic oxygen to keep the residue neutral then wouldn't it be convenient to think as if it's a radical ? On Wed, Oct 3, 2012 at 4:42 PM, Justin Lemkul wrote: > > >

Re: [gmx-users] tyrosyl radical force field

On 10/3/12 6:00 AM, tarak karmakar wrote: Dear All, Is it possible to deal a protein with tyrosyl radical in Molecular Dynamics Simulation ?? If possible can you please provide me the reference or literature where I can find the force field parameters for tyrosyl radical ? Molecular mechani