[AMBER] PCA trajectories give unrealistic structures

From: Gulsevin,Alican <agulsevin.chem.ufl.edu>
Date: Wed, 9 Nov 2016 16:06:43 +0000

Hello Dear Amber Users,

I'm running into some problems with the PCA procedure. What I'm investigating is structural changes induced on a receptor by binding of a number of ligands, taking an unliganded simulation as my reference structure. I run the MD structures separately for ligands and the unliganded structure, and then I follow the corresponding Amber Tutorial as my main guide (http://www.amber.utah.edu/AMBER-workshop/London-2015/pca/)<http://www.amber.utah.edu/AMBER-workshop/London-2015/pca/> and calculations end without any errors. When I run PCA with two structures, what I get is a nice output trajectory where I see loops moving around. However, when I use five structures, what I see in the trajectory is an unrealistically contracted protein growing into a normal size protein, which clearly is not a representation of what's really going on. I have two questions at this point:

1) Why do I keep seeing this weird trajectory with 5 ligands, but not with 2? All structures are referenced to the same pdb structure and prmtop files are the same (because proteins are identical in all cases). Is CPPTRAJ PCA designed to compare two structures only by its nature, or is there another step necessary in addition to what's described because I'm using multiple MD results?

2) Is there a way to get a pretty PC1 vs PC2 kind of plot using CPPTRAJ? A reply to a past question suggests keyword "projection", but I wonder if it's compatible with the kind of analysis I described, again for a larger number of trajectories.

Thanks for the help from now,

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Received on Wed Nov 09 2016 - 08:30:02 PST
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