We are doing a molecular dynamic simulation with GROMACS using the AMBER force field. During the simulation the disulfide bonds are increasing over time. We set the bridge manually with pdb2gmx Why is this happening?
Hi, Cecilia,
you ser ter distances between sulfur atoms increasing during simulations? Have you also measured this increase? If yes, check on top file if there is indeed a bond between them. If not, you can add the bond term manually in the topology file.
Most probably sulfur atoms of the cysteines making the SS bridge are not bonded in the topology file because it is not expected that a MD simulation breaks a covalent bond. Check in the topology file whether these cysteines are in the SH form in which case you must fix them by defining the SS bond
Agree with Dr. Pacios. The name of CYS residue should be changed to CYX for disulfide bonds in the PDB file when you prepare the PRMTOP file in AMBERTOOLS. And you need to BOND the two S atoms in TLEAP. Please check my blog at https://sunxiaoquan.wordpress.com/2015/02/12/prepare-prmtop-and-inpcrd-for-glycoprotein-in-ambertools14/. I think you did not do that, so the disulfide bond is meaningless.
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