What is the best way if I wanted to study Molecular Dynamic Simulations of 20 inhibitors with two different isoforms of a protein in a stipulated time?
If you are looking for a software to easily set up MD simulations, I suggest
YASARA http://www.yasara.org/news.htm it is simple to set up simulations and runs very fast
Try NAMD (http://www.ks.uiuc.edu/Research/namd/) or Desmond (http://www.deshawresearch.com/downloads/download_desmond.cgi/) other options would be TINKER http://dasher.wustl.edu/tinker/
Abalone http://www.biomolecular-modeling.com/Abalone/index.html
For Inhibitors embedded DREIDING like a force field can be used (default option), for protein Amber99SB or Amber03.
The only thing to parameterize inhibitor is to calculate the partial atomic charges.
The choice depend on what system you work with. You can browse the internet and see which is suitable for your system. Personally I think NAMD is an easy program for beginner to understand and try by theirself. it is also free to download. A lot of tutorial and example are given in their website.
http://www.ks.uiuc.edu/Research/namd/
Hi, If you are looking for a software to easily set up MD simulations, I suggest TINKER http://dasher.wustl.edu/tinker/
thank you all
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