AMBER Archive (2008)

Subject: Re: AMBER: pmemd iwrap trouble

From: Thomas Cheatham III (tec3_at_utah.edu)
Date: Tue Aug 26 2008 - 11:48:04 CDT

> I get exactly the same results from pmemd9, pmemd10, and sander10 in
> regard the wrapping (iwrap=1); 2 of my subunits are displaced
> (regardless of ioutfm=1 or 0). However, by using the following ptraj
> script (instead of iwrap) it results in a truncated octahedral fitted
> nicely around the protein complex (as expected):
>
> center :1-5332
> image center familiar
> trajout reimaged.rst restart
>
> However, I see no trouble when I use solvatebox instead of solvateoct
> (for both sander and pmemd). Unfortunately I cant go back using
> solvatebox at this time, after 2 months of simulations..

I've been following this thread and think that it is just a
misunderstanding and that nothing is wrong with the imaging, it just
doesn't look like you would expect. sander/pmemd image in triclinic space
so for a protein this looks like a slanted box with the protein
potentially sticking out...

   __PPP__
  / PPP /
 /___PPP/

...rather than the more "familiar" truncated octahedron shape. To verify
this, look at the ptraj imaged trajectory without the familiar keyword;
this will look like what you are seeing from sander/pmemd and they are
equivalent, albeit different ways of looking at things.

There is also a way in pmemd to generate images in alternative unit cells,

image xoffset 1.0 yoffset 0.0 zoffset 0.0

which you can do for each direction and then "see" the whole packing in
the unit cell.

If you are still concerned, you could also try a single point energy
minimization on both the "familiar" and alternative restrt file to verify
the energies are similar.

imaging in ptraj is not broken (now) to the best of my knowledge; there
was a brief problem with AmberTools 1.0 that lead to errors in the box
size, but this was working in earlier versions and is working in current
versions.

--tom

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