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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