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

Jochen Hub jochen at xray.bmc.uu.se
Fri Nov 20 14:01:28 CET 2009


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.

...C-S-H  H-S-C...

... 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,


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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