GROMACS version: 2018.1
GROMACS modification: Yes/No
I a trying to create disulfide bond between the two cysteine residues in my protein.
I used the following command:-
gmx pdb2gmx -f wt.pdb -o wt.gro -p wt.top -ignh -ss -merge all
This distance between the bonds is 0.202nm.
However, I am not able to see the formation of disulfide bonds in the structure file (wt.gro) as well as the topology file (wt.top)
The files can be assessed at the following G Drive link:-
https://drive.google.com/drive/folders/1SAFYH-q59qLHwUUdz0XPsbWUbmc2YeTZ?usp=sharing
I will appreciate any help in this regard.
Thanks in Advance