--- Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Francesco, There is no feature yet in Chimera to plot values (such as RMSD) vs. time for a trajectory, sorry.
I hope you may plan to offer such useful tool.
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,
I may have better waited until I understand what you suggest. It is the hope to further clarify my things that urges me to ask for that explained with other words. I don't understand where to look at.
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 judgment when viewing the trajectory is a better tool than some numerical cutoff for deciding if it is reasonable or not.
That is reassuring. As I said, things "at the naked eye" look like OK. And the judgment is competent because the ligand is an organic structure I am familiar with. No repeating unit, special bond lengths and orientations, no common stuff.
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,
It was carefully heated to 300K and equilibrated removing restraints step by step, i.e., first by the lipid, then by the protein-complex. If anything, I am not sure if my procedure of removing the strong restraint on the protein and ligand abruptly is correct, or if a smaller force should have been applied first. It is not easy to grasp such information from the literature.
or perhaps if the RMSD just keeps increasing throughout the trajectory,
I am acquiring experience on these affairs. As far as I presently understand, RMSD is not increasing along the trajectory. Well, a plot of RMSD vs time would be the best answer. Thanks francesco
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 trajectory. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ ensemblematch/ensemblematch.html
Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
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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