[gmx-users] Thioester bond problem

Justin A. Lemkul jalemkul at vt.edu
Fri Nov 4 19:34:53 CET 2011

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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