Disulfide bond disappeared after energy minimisation

OpenMM Zephyr provides a visual application for running GPU-accelerated molecular simulations.
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Anderson Wang
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Joined: Fri Feb 24, 2012 11:50 am

Disulfide bond disappeared after energy minimisation

Post by Anderson Wang » 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
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