One difference: tleap considers the two Na+ ions to be part of the solute. Sleap puts them in the solvent.
I can see arguments both ways... but, that might be part of the issue.
:-) 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: Wei Zhang [zgjzweig.gmail.com]
Sent: Friday, April 08, 2011 2:17 PM
To: AMBER Developers Mailing List
Subject: Re: [AMBER-Developers] Problems with sleap and iwrap
Hi Ross,
I was trying to run the script run_MDEQ.sh, but it is missing a file "fixedgroups".
Can you send the other file so I can reproduce the error?
and I agree with Jason and Lachele that the problem seems to be with the section "SOLVENTS_POINTER"
Sincerely,
Wei
On Apr 8, 2011, at 11:58 AM, Ross Walker wrote:
> 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
> be read every day, and should not be used for urgent or sensitive issues.
>
>
> <originalt.pdb><leaprc_pdb_tleap.txt><leaprc_pdb_sleap.txt><run_EQMD.sh>_______________________________________________
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Received on Fri Apr 08 2011 - 12:00:03 PDT
