Re: [gmx-users] Free energy perturbation of Cu(I) binding

Thank you David I would certainly try this way. On Mon, Feb 9, 2009 at 1:08 PM, David Mobley wrote: > Hi, > >> Thanks David, But if I just remove the Copper atom and do the >> simulation as copper is charged there would be sudden change in >> electrostatics and the protein started unfolding when

Re: [gmx-users] Free energy perturbation of Cu(I) binding

Hi, > Thanks David, But if I just remove the Copper atom and do the > simulation as copper is charged there would be sudden change in > electrostatics and the protein started unfolding when I ran the > simulation for 10ns. So I thought perturbing the charge by little > every time I can get a struc

[gmx-users] Free energy perturbation of Cu(I) binding

You might benefit from reading Mobley, Chodera, and Dill. J. Chem. Theory. Comput. 2007, 3, 1231-1235. This paper doesn't relate exactly to your question, though, unless you do something like David initially suggested here http://www.gromacs.org/pipermail/gmx-users/2009-February/039436.html

Re: [gmx-users] Free energy perturbation of Cu(I) binding

abhigna polavarapu wrote: Hey Mark, I am just not getting the theory behind doing position restraints and applying them to equilibrate. Sure... so that's why I recommended chapter 5 (which has an example of position restraints in section 5.7.1, which you can understand with references to the

Re: [gmx-users] Free energy perturbation of Cu(I) binding

Hey Mark, I am just not getting the theory behind doing position restraints and applying them to equilibrate. So let me frame my question well. Cu(I) is binding to three amino acids in the protein. Now If I remove Cu(I) the -1 charge of the protein changes to 0. So the protein has two specific cha

Re: [gmx-users] Free energy perturbation of Cu(I) binding

abhigna polavarapu wrote: Thanks Mark, thats what I really wanted to do. So can you please let me know where I can find out the way to do position restraints and to know how these work. Chapter 5 in the manual, or some tutorial material (perhaps from the wiki). Mark ___

Re: [gmx-users] Free energy perturbation of Cu(I) binding

Thanks Mark, thats what I really wanted to do. So can you please let me know where I can find out the way to do position restraints and to know how these work. abhigna On Tue, Feb 3, 2009 at 10:18 PM, Mark Abraham wrote: > abhigna polavarapu wrote: >> >> Thanks David, But if I just remove the Co

Re: [gmx-users] Free energy perturbation of Cu(I) binding

abhigna polavarapu wrote: Thanks David, But if I just remove the Copper atom and do the simulation as copper is charged there would be sudden change in electrostatics and the protein started unfolding when I ran the simulation for 10ns. So I thought perturbing the charge by little every time I ca

Re: [gmx-users] Free energy perturbation of Cu(I) binding

Thanks David, But if I just remove the Copper atom and do the simulation as copper is charged there would be sudden change in electrostatics and the protein started unfolding when I ran the simulation for 10ns. So I thought perturbing the charge by little every time I can get a structure with more

Re: [gmx-users] Free energy perturbation of Cu(I) binding

Perhaps this is obvious, but typically you only want to do free energy perturbation if you are interested in computing a free energy difference. If you are merely interested in structural properties of a different system (in this case, the protein without the copper there) you can simply make the c

[gmx-users] Free energy perturbation of Cu(I) binding

Hi all, Thank you for the help till now and I successfully generated the forcefield Cu(I) binding protein. Now I wanted get the structure of non-copper bound form which I think I can do by perturbing the charge on Cu(I) and even perturbing the bonded and nonbonded parameters. Is there a