I would like to perform MD simulation study for CYP450 proteins in gromacs 4.6.7 with gromos53a6.ff. When I prepare the system for simulation, i have got error that gb_, ga_ and gd_ were not found for cystein linking to the heme molecule. These parameters don't exist in the gromos53a6 force field. Therefore based on data from literature I pass missing parameters to ffbond.itp file, but during generating topology file, these bond was no included in topology file. I wonder what could be reason of this failure, and how to fix it.
Does any one know what should I do. Thanks in advance for your valuable time.
Dear Tomasz
As far as I know, OPLS-AA and Amber force fields are better for protein simulations. You can consider those force fields and hope it works without any errors.
Dear Jamoliddin,
Thank You for You reply, I know that amber and OPLS-AA are better for protein-ligand simulation, but I want to immersed my CYP P450 in lipid membrane and base on literature I saw that author were used the Gromos53a6 force filed. Base on Your answer is there any server with equilibrate membrane for Amber or OPLS-AA force field?
53A6 under-stabilizes helices; it may be useful for disordered proteins but should not be used for much else. If you're set on a GROMOS force field, at least use 54A7 in which this problem was fixed. United-atom, GROMOS-compatible lipid force fields are also not the best choice, something like Slipids (with AMBER) or CHARMM36 would be much better nowadays. If you upload your system to CHARMM-GUI, it should be able to build everything for you, including the membrane (and it will provide you with a GROMACS topology for everything).
Even if you get pdb2gmx to work, there will likely be incorrect angles and dihedrals as a consequence of the way the generation is done; you'll have to manually edit the topology to correct for these.
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