antonio wrote:
Dear gromacs users
I am trying to carry out a free energy perturbation to evaluate the
difference in binding energy between two inhibitors of the same protein.
I have read a lot of post but i did no understand how to create the
topology file.
have i to write a mixed pdb of the tw
I will try the second solution you proposed (which seems more flexible).
So, I should edit the top file (as explained in the "Topologies/File
formats/Topologies for free energy calculations" section of the
manual). And I should NOT use "couple-moltype" anymore, which is just
a shortcut for the sta
> From: giovanni.bu...@gmail.com
> Date: Mon, 14 Dec 2009 13:47:37 +0100
> To: gmx-users@gromacs.org
> Subject: [gmx-users] free energy perturbation
>
> Dear all,
>
> I am using GROMACS with free-energy perturbation to switch off a
> molecule gradually. If I understand correctly, the parameter
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
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
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
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
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
___
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
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
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
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
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