Dear all,
I am currently working on a protein simulation with a heme group in the protein. I am wondering whether anyone can tell me how I can set it up in GROMCAS with charmm forcefile, since error shown when I generated topology files. Thank you.
Hi Hong Li,
The heme consists of the Fe atom at the center of the porphyrin ring. I guess the CHARMM force field lacks parameters for the iron atom, leading to an error. I recommend using the AMBER force field, which allows you to parameterize the heme for simulation. You can prepare the system using the AmberTools package by following this tutorial:
https://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.php
Once you've completed the preparation, you can use the Python script ParmEd to convert the AMBER topology to the GROMACS topology and perform MD simulation.
Heme parameters are already present in charmm36. You can prepare protein bound to heme easily in gromacs.
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