Installing vina

Re: Installing vina

Postby dfarrow » Fri Nov 18, 2011 11:47 am

In case anyone was having the same problem as me, here's how I fixed it:

It turns out that the version of OpenBabel that I installed from the apt repo was 2.2.3. That version doesn't support the pdbqt format, and so it was blowing up when it tried to process my pdbqt file.

Newer versions of OpenBabel (2.3.0+) have pdbqt support, so I ended up downloading the source code of the latest version (2.3.1) and compiling it myself.

@Ted - Yes, I modified the new perl script with my local SCRIPTPATH.

Re: Installing vina

Postby troman » Sat Nov 19, 2011 2:59 pm

Upon filtering for clashes, a lot of my ligands still get distance too far from crystal messages. How/why would this happen?

Re: Installing vina

Postby dkoes » Sat Nov 19, 2011 4:17 pm

There may still be some minor steric clashes. Alternatively, there may be electrostatic clashes. For example a positive charge on the receptor is adjacent to a positive charge on the ligand. This can push ligand out of the pocket. You can try reducing the clash depth of the filter, but you probably lose some good hits whose minor clashes can be easily resolved by minimization.
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