[gmx-users] Disulfide bridge formation between A and B state

Berk Hess gmx3 at hotmail.com
Fri Nov 20 14:51:27 CET 2009


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.


> Date: Fri, 20 Nov 2009 14:01:28 +0100
> From: jochen at xray.bmc.uu.se
> To: gmx-users at gromacs.org
> 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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