Disulfide bond disappeared after energy minimisation
Posted: Wed Mar 21, 2012 4:26 pm
Hi, everyone,
I am very new to Molecular Dynamics and was hoping someone can help me with this issue that I encountered. I have been trying to do some MD runs with my protein structure, which contains a functionally important disulfide bond, using OpenMM Zephyr. However, the disulfide bond disappeared after the energy minimisation step. While I attempted to skip the energy minimisation step, the trajectory after he MD couldn't be saved. I also tried to play around with different force fields (Amder99sb and 03), but neither worked. The trajectory can only be displayed and saved when enery minimisation and Amber96 are selected. I have tried on other disulfide containing crystal structures, but they all ended up the same fate. Can some one please advise on this? Many thanks in advance.
Regards,
Anderson Wang
I am very new to Molecular Dynamics and was hoping someone can help me with this issue that I encountered. I have been trying to do some MD runs with my protein structure, which contains a functionally important disulfide bond, using OpenMM Zephyr. However, the disulfide bond disappeared after the energy minimisation step. While I attempted to skip the energy minimisation step, the trajectory after he MD couldn't be saved. I also tried to play around with different force fields (Amder99sb and 03), but neither worked. The trajectory can only be displayed and saved when enery minimisation and Amber96 are selected. I have tried on other disulfide containing crystal structures, but they all ended up the same fate. Can some one please advise on this? Many thanks in advance.
Regards,
Anderson Wang