[gmx-users] Thioester bond problem

alberto arrigoni arrigonialberto86 at gmail.com
Fri Nov 4 18:23:58 CET 2011

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.
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