On Fri, Apr 8, 2011 at 10:42 AM, B. Lachele Foley <lfoley.uga.edu> wrote:
> We haven't seen that, particularly, but none of us would be surprised. We
> stopped trusting sleap a while back (Arunima is nearly done hacking 1-4
> scaling into tleap...).
>
Nice.
>
> We're also working on a top-file checker that, with luck, will be able to
> find the problem. That's a couple weeks out, but we can implement some bits
> now, such as internal box-info checks, if they will be useful. Can rdparm
> help about the top file? Our checker will read a prmtop and associated
> param files and make sure everything is sane and consistent.
>
The issue that Ross is pointing out is an imaging artifact. Luckily (or
unluckily?), there are only a small number of things in the prmtop file that
actually affect imaging:
The value of IFBOX (that tells what kind of box it is), and the molecule
information, found in %FLAG SOLVENT_POINTERS and %FLAG ATOMS_PER_MOLECULE,
as imaging is done on a per-molecule basis.
The IFBOX problem is an issue that needs to be fixed, but is overall easy to
fix and not much of an issue. The more sinister problem would be with
borked ATOMS_PER_MOLECULE and SOLVENT_POINTERS sections; this would be much
harder to track down and could present ugly ugly issues.
--Jason
> Sleap combines parameters that are the same, but apply to different atom
> types. That might be confusing something in pmemd. I can't think of
> anything else at the moment.
>
> :-) Lachele
>
> Dr. B. Lachele Foley
> Complex Carbohydrate Research Center
> The University of Georgia
> Athens, GA USA
> lfoley.uga.edu
> http://glycam.ccrc.uga.edu
>
> ________________________________________
> From: Ross Walker [ross.rosswalker.co.uk]
> Sent: Friday, April 08, 2011 12:58 PM
> To: AMBER Developers Mailing List
> Subject: [AMBER-Developers] Problems with sleap and iwrap
>
> Hi All,
>
> Has anybody experienced problems with sleap and iwrap? (Is anybody using
> sleap routinely?).
>
> Attached is a pdb file and two scripts that 'should' do the same thing in
> sleap and tleap. If you then run MD with the two resulting prmtop and
> inpcrd
> files things appear to be fine without iwrap=0 but if you set iwrap=1 the
> sleap generated prmtop run behaves VERY strangely.
>
> You get the protein jumping out of the water box in a strange way. For this
> case with just one molecule things appear to be ok, as in just a strange
> imaging issue. However, if you set a system up with glycans attached then
> in
> the sleap run only half the molecule gets imaged and then it crashes with
> vlimit errors (due to bonds being massively stretched) as soon as you turn
> on iwrap.
>
> Hence it seems like there is something very wrong with the prmtop generated
> by sleap. This is BAD since sleap is the only way to generate prmtops with
> mixed 1-4 scaling parameters in right now.
>
> Has anybody else seen such issues / has an idea of what might be wrong with
> the sleap prmtop?
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Assistant Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
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>
>
>
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Apr 08 2011 - 11:00:05 PDT
