Hi, I'm modeling a prolipoprotein to run an MD simulation. I'm trying to add DAG to cysteine using structure editing tools on chimera but I've been unsuccessful. Appreciate if anyone can help with the matter. Thanks in advance!
Open both protein and ligand in the same Chimera panel, move the ligand to your position of choice [Favourits > Model Panel (deactivate one item)], and create a bond between heavy atoms [Tools > Build structure (you can find multiple options there)], and minimize the structure [Tools > Structure Editing > Minimize].
Finally, save as a single molecule.
For MD simulation, you need to create a new cystein entry in ForceField with DAG atoms and you need to parametrize this new specie.
Thanks for the replies!
I've actually created the bond between two models using Chimera and it worked! but I haven't been successful at minimizing the structure. Probably my Chimera lack a certain plug in. What I did was using the structure to run MD simulation but the bond was broken during topology preparation.
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