alberto arrigoni wrote:
Dear Gromacs users,
I'm attempting to simulate a system composed of two proteins containing
a thioester bond between the C-terminus of chain A and a cysteine
residue from chain B.
I wonder if the parameters for this bond to be included in the .top
file exist. Also, I am having troubles figuring out how to include them,
since the thioester generates a branch between the two chains.
A possible strategy I have come up with is to use specbond.dat in order
to create a bond, and then try to add by hand the parameters in the .top
file. The problem with this would be to erase an hydroxyl group from the
C terminus and a hydrogen atom from the sulfidrilic group. Also, with
"specbond.dat" (even changing cutoffs) the target bond is not the only
one that is created by pdb2gmx, since unfortunately another cisteine is
closely located to a glicine residue (the same residue I have in
C-terminus).
I am very grateful for any assistence you could provide.
There are several things I can think of to try. First, have you used the
"-chainsep ter" option in pdb2gmx? It shouldn't create termini based on chain
identifiers, but rather on TER entries, which, if removed, don't create
problems. You can also use the -ter option to interactively select termini
states, thus adding no terminal acid group atoms to the actual C-terminus of the
first chain.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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