I performed in-silico acetylation using PyTM plugin but there are certain clashes that I want to resolve. I couldn't perform energy minimization using gromacs, chimera as they do not have default parameters to deal with acetylated residue. Further Vienna ptm, force-field is not compatible with the latest gromacs version. I tried yasara minimization, but the number of clashes increased.
Can anyone suggest some ways that I could resolve these clashes or any software/ webserver to perform in-silico acetylation.
You need to get the appropriate force field parameters and topology files for the modified amino acids, e.g. from this server:
http://vienna-ptm.univie.ac.at/
Article Vienna-PTM web server: a toolkit for MD simulations of prote...
Here are CHARMM parameters for methylated lysines and arginines, and acetylated lysine. Though, if all you need is to energy-optimize your structure then the OPLS force field would do it.
Article Force Field Parameters for the Simulation of Modified Histone Tails
I think if the purpose is to just get an acetylated version of your protein, then Vienna-PTM is sufficient for that. Apart from generating parameter files of MD (if you need that), it also gives the energy minimized structure. You just need to enable the "Minimize" option down there in the Set Parameters section which is disabled by default.
Dmitri Kireev Sir, what if energy minimization has to be done using Discovery Studio?
Ishita Shreshtha You can do it in DS. Use a general purpose force field, such as, MMFF.
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