to Vienna-PTM, a resource for exploring protein post-translational modifications (PTMs) using molecular dynamics (MD) simulations! Here, you can modify a protein PDB file of your choice with one or more supported PTMs and obtain force field parameters (GROMOS 45A3, 54A7 [ref] and 54A8 [ref]) and input files needed to perform MD simulations of the modified proteins using the GROMACS package [ref]. Currently, we support a total of 260 different enzymatic and non-enzymatic modifications.
If you use Vienna-PTM server or the associated PTM parameters for your work, please cite:
- Margreitter C*, Petrov D* & Zagrovic B (2013) "Vienna-PTM webserver: a toolkit for MD simulations of protein post-translational modifications" Nucleic Acids Research, 41, W422-426 [link].
- Petrov D*, Margreitter C*, Grandits M, Oostenbrink C & Zagrovic B (2013) "Development and verification of force-field parameters for molecular dynamics simulations of protein post-translational modifications" PLOS Computational Biology, 9(7), e1003154 [link].
- Margreitter C, Reif M & Oostenbrink C (2017) "Update on phosphate and charged post-translationally modified amino acid parameters in the GROMOS force field" Journal of Computational Chemistry, 38(10), 714–720 [link].
The parameter set 54a8 in the GROMACS format had serious flaws (the canonical amino acids have not been updated accordingly). Please download and use the new version (1.9.0). If you have any questions, please do contact us directly via firstname.lastname@example.org.