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...).
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.
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 |
---------------------------------------------------------
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Received on Fri Apr 08 2011 - 11:00:02 PDT
