Showing posts from December, 2015

Native contact (Q) biasing in GROMACS and plumed2

Fraction of native contacts is a pretty darn good coordinate for looking at protein folding, definitely when it comes to small proteins. Just have a look: Fraction of native contacts can be used to analyze long, unbiased MD runs – like those from DESRES – or in biasing simulations. But how does it fare when used in biasing? Well I don't know – but you can now find out by yourself! Either in umbrella sampling or metadynamics – or a method of your choice that doesn't use energy as your collective variable. Here, I'm happy to report that I incorporated an implementation of native contact CV into plumed2 – an enhanced sampling package that can be used with a number of popular MD simulation engines. The pull request is now closed and it's likely that the next release of plumed2 will include this. "Tutorial" is a regression test in plumed2 sources   regtest/basic/rt

Scripting access

Below is a simple python script that allows one to programatically access, a small-molecule parametrization service. Autocorrect said "problematic" instead of "programatic", maybe I'm noting getting the hint... The script has minimal dependencies and is very "light-weight", meaning no error handling or error messages. A full working example for a benzene (duh!) is attached. Long time ago, I had to implement something similar to this script, so this was a fairly easy job. It relies on mechanize and beautiful soup to do it's thing. python -u "YOUR USERNAME" -p "YOUR PASSWORD" -c benzene.pdb # manually correct the "RESI" line in benzene.str to be  # RESI BNZ 0.000 ! param... python BNZ benzene.mol2 benzene.str charmm36-jun2015.ff/ Source code and examples git clone Example on google drive Edited: note on errors, link to gi