AMBER Archive (2009)

Subject: Re: [AMBER] problem in rmsd

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Mon Mar 09 2009 - 22:48:53 CDT

> I output PDB files for each frame. interesting thing is when I
> choose the option "new cartoon" in vmd, then the figure disappears.
> But when i created the pdb file from the last rst file, it looks
> reasonable while I visualize in VMD. What puzzles me, why these 3rd &
> 4th frame only give absurd rmsd irrespective of ntwx=1 or ntwx=50.

This suggests some kind of mismatch in what vmd expects and what you are
feeding it. You are looking at the PDB files, each in turn?

*If* the frames were 300A away (which is highly unlikely if the rst is
fine), perhaps you wouldn't see them in the vmd window... I also am not
an expert in VMD so do not know what "new cartoon" means. If it is only
frames 3 and 4 that are off, something is indeed odd. If the rst was
still good, I would think file corruption. To dig deeper, I would go back
and look at each frame, sequentially:

trajin mdcrd 1 10 1
trajout snapshot pdb

will generate snapshot.1, snapshot.2, ...

Look at the 10 pdb files produced. You should be able to see what is
happening. If the structure becomes garbage, and the rst is fine, then it
is file corruption (or prmtop mismatch) or some such.

We can continue this off-list. --tec3

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