[Chimera-users] Fwd: Re: Bug (?) with EnsembleCluster

Elaine Meng meng at cgl.ucsf.edu
Wed Jan 16 10:07:05 PST 2008

Hi Francesco,
There is no feature yet in Chimera to plot values (such as RMSD) vs.  
time for a trajectory, sorry.
If you look at just the top tiny line in the RMSD map (frame 1 vs.  
all the others) it contains that information in terms of color, but I  
agree that is not as easy to look at as a plot.

I don't know what happened in VMD; maybe there was some error.

It is difficult to say what value of RMSD would correspond to too  
much variation.  The values you gave don't sound that high to me, but  
probably your judgement when viewing the trajectory is a better tool  
than some numerical cutoff for deciding if it is reasonable or not.   
Does the interaction observed in your trajectory agree with any  
experimental data on what residues contact the ligand?  Or if you  
started with an experimentally determined structure of the complex,  
does it stay in approximately the same binding site? (sounds like it  
does)  Another thing to consider is that often people start with a  
minimization to remove any severe strains or clashes, then some  
equilibration MD before the production MD.  It depends on whether  
your system is already equilibrated, or perhaps if the RMSD just  
keeps increasing throughout the trajectory, the system is unstable  
and will not equilibrate.

The following I mainly mention for completeness... it may not be  
helpful in your case:
There is another tool, EnsembleMatch, that shows the RMSD values as  
numbers (instead of a color map) for an all-by-all comparison of two  
ensembles, but it is only good for much smaller sets of structures.   
For example, you could compare one structure (frame 1, or crystal  
structure if you have it) to a sample of maybe 10 structures from the  

Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 16, 2008, at 8:19 AM, Francesco Pietra wrote:

> Yes, the two behave differently, and not only as to importing pdb.
> I had opened my combined trajectories (protein+ligand in a lipid  
> membrane) in
> VMD while looking at either the ligand or the protein: both highly  
> distorted at
> each one of the 550 frames. I only got nearly reasonable structure  
> for the
> ligand by averaging the frames. That was most discouraging in the  
> last few
> days. Did the same for the equilibration and got the same  
> discouraging results.
> This last analysis was not fitting the analysis with ptraj,
> Therefore I have now done the same for the MD trajectories with  
> Chimera, which
> runs more slowly along the frames, and surprisingly, "at the naked  
> eye" both
> the ligand and the protein save their correct structure along the  
> 550 frames,
> with only the internal displacement on/back that one expects from  
> MD. I
> repeated without hiding the membrane and water, and "at the naked"  
> the ligand
> was not wandering around.
> I looked at RMDS Maps(Start frame 1; End 550; Step size 2; RMSD map of
> trajectory against itself; Lower rmsd threshold 2.9, higher 3.9:  
> RMSD varied
> from 0.194 to 1.810 for the ligand and from 0.612 to 2.420 for the  
> protein. Is
> that variation too much for accepting this MD for good (or fair)  
> and continuing
> it with same settings? If it is a too large a range, that explains  
> why the
> ligand encountered so many protein residues when the mask was used.
> I was unable to find how to get a plot of RMSD against time. I  
> would like to do
> that for the ligand (which is a single big residue) and selected  
> residues of
> the protein.
> Thanks
> francesco

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