Hi all,
I am trying to simulate a protein containing a modified Lysin : Trimethyllysine. I am a NAMD user and I couldn't find a proper forcefield (topology and parameter files) with charmm yet.
any suggestions?
Thanks a lot
Farzaneh
The force field for methyllysine can be obtained from the authors of this article:
Article Force Field Parameters for the Simulation of Modified Histone Tails
Grauffel, C. , Stote, R. H. and Dejaegere, A. (2010), Force field parameters for the simulation of modified histone tails. J. Comput. Chem., 31: 2434-2451. doi:10.1002/jcc.21536
When you modify a standard residue like an amino acid, it's considered as a non standard residue like a ligand - so, you must use the same way that you deal with any ligand, with a difference that here there's a covalent bond formed between the standard and non standard residues. Here, not only the modified Lysin is a non standard residue but also the amino acid which is bound to it.
This can be helpful:
https://www.ks.uiuc.edu/Training/Tutorials/science/forcefield-tutorial/forcefield.pdf
If you are working mostly with non standard residues, I strongly recommend you to use Desmond code for your MD simulations. This code was written to generate potentials for non standard residues automatically.
Regarding non standard non residues, Desmond does not need users to manually generate potentials - there is a very simple script that can do it using OPLS force field.
But NAMD or other MD codes need to do it manually.
All the MD codes do the same thing but the only things that make them different or even user friendly are the scripts coded to help users to deal easily with parameter generating. There's no any potential parameters for non standard residues, including small ligands or other unknown compounds, in force field data base. But there are some scripts that can find appropriate parameters using standard parameters in Amber, OPLS or others......
Thanks Ramin. I had a look at user guide. Viparr part is for nonstandard residues. also "to more accurately simulate the behavior of water or other molecules, certain force fields add electrostatic or van der Waals interaction sites located where no atom is". pseudoparticles without mass but with charge. Cool!
Thank you for make it clear Stéphane. I measure some parameters manually and I guess the only way for difficult cases is paramChem and similar approaches.
One advantage of using Gromacs could be this one.
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