Hi Berk,
thanks a lot for the comment.
Actually I have found a solution which is good enough for what I am
planing to do. I have placed a dummy onto the sulfur which is turned on
while the sulfur is tuned off. And I switch on a bond between the dummys
when switching from A to B. Then I have added all the necessary
exclusions and pairs between the dummy and the nearby atoms, and the new
angles and dihedrals due to the S-S bond.
The only issue which is now not exact are the 1-4 coulomb interactions
of the dummies in the B state. They are computed completely instead of
being scaled down by 1.2. So for a real FEP calculation that might be a
problem, but for me it is fine.
Cheers,
Jochen
Berk Hess wrote:
Hi,
I would say that it is very uncommon to form a bond during free energy
calculations.
To make this work easily we would need to introduce a pair interaction
with all parameters explicit
that can be perturbed.
For the moment you should be able to get it to work using tabulated
bonded interactions.
The only thing that is not supported through that are soft-core
interactions, but I guess
those will not be necessary for 1-4 interactions.
Berk
> Date: Fri, 20 Nov 2009 14:01:28 +0100
> From: [email protected]
> To: [email protected]
> Subject: [gmx-users] Disulfide bridge formation between A and B state
>
> Hi,
>
> I have yesterday already started a topic, but I think I was a bit
> unclear about what is the problem.
>
> I want to have a disulfide bridge in the B state, but not in the A
> state. And I have not found a way to get the Coulomb interaction
between
> the two sulfurs (and other nearby atoms) right in the A and in the B
state.
>
> A-state:
> ...C-S-H H-S-C...
>
> B-state:
> ... C-S-S-C
> | |
> H H (where these two H are dummies in B)
>
> To close the S-S bond smoothly by going from lambda=0 to 1, I have
added
> a bond type 6 (harmonic potential)
> [ bonds ]
> S-nr S-nr 6 b0 k
> and, a bond type 5 (connection without interaction)
> S-nr Snr 5
> That is required since otherwise, I will have full LJ interaction in B
> state between, e.g. between the two sulfurs. To have correct LJ
> interaction in A, I have added pairs between all required atoms, so the
> LJ should be fine.
>
> But what about the charges? If I have a connection between, e.g.,
> sulfur1 and sulfur2, I will never have a coulomb interaction. The
> problem seems that there is no way to scale a coulomb interaction
> between two atoms between A and B. There is a pair type 2, that
> apparently allows to add 1-4 charge interactions, but the parameters
> cannot be scaled between state A and B (manual table 5.4).
>
> I feel that forming a bond with the FEP should be more or less common
> thing, that's why I am surprised that there seems to be no solution for
> that. Or am I missing something here?
>
> Any ideas?
>
> Thanks a lot,
>
> Jochen
>
>
>
> --
> ---------------------------------------------------
> Dr. Jochen Hub
> Molecular Biophysics group
> Dept. of Cell & Molecular Biology
> Uppsala University. Box 596, 75124 Uppsala, Sweden.
> Phone: +46-18-4714451 Fax: +46-18-511755
> ---------------------------------------------------
>
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Dr. Jochen Hub
Molecular Biophysics group
Dept. of Cell & Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4714451 Fax: +46-18-511755
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