I have a PDB file of a heterodimer with acetylated K40. Which force field should I use to simulate it using GROMACS?

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Raag Saluja

Thank you, Stephane. I have simulated the heterodimer before. I have also done in silico site directed mutagenesis and simulated the mutants. So I am not worried about the computational resources part. What I am worried about, however, is that I am getting a "fatal error" with all 15 of the GROMACS force fields, as soon as I acetylate the molecule.

Vikash Kumar

You are getting error message because available force fields in the GROMACS do not support acetylated residue. You can add parameters for the modified residue in the parameter files. Please read the given article.

http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003154