AMBER Archive (2008)

Subject: Re: AMBER: pmemd iwrap trouble

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Aug 26 2008 - 11:57:28 CDT

Hi Tom,
would that bug be the reason why some of my frames aren't imaged
properly and some are?
never had trouble with imaging sander traj files, but that may have
been older ptraj.
I should download the ambertools update and try it but I'm on the road
so hard to do unless you think that's the problem I'm having.
carlos

On Tue, Aug 26, 2008 at 12:48 PM, Thomas Cheatham III <tec3_at_utah.edu> wrote:
>
>> 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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-- 
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Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
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Stony Brook University E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
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