In MD simulation, I see that the peptide loses its disulfide bond as a result of high temperature application. I can't see the disulfide link in PyMOL, but I can see a link with the SG code in the GRO file. I am making visualization using GRO file and XTC file. Am I making a mistake in an application or is it normal that I cannot see the disulfide bond in a high temperature application?
Hello Büşra,
Even you are using high temperature MD simulation the disulfide bond will not break unless you use QM/MM.
1. How you prepared your disulfide bridge may be residue name issue. I am not gromacs user but in amber if you need to make bond you need to replace CYS to CYX.
https://www.researchgate.net/post/Do_we_have_any_parameter_for_CSX_residue_in_Amber
2. Secondly check you initial structure.
3. measure the distance between SG-SG bond.
4. Use any other software like VMD (Sometime software problem).
Hopefully it will help.
Regards
Aashish
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