On Fri, Apr 8, 2011 at 9:58 AM, Ross Walker <ross.rosswalker.co.uk> 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.
>
Yes, I've seen this before. Check the value of IFBOX produced by both sleap
and tleap. I thought this bug had been fixed awhile ago... what version of
AmberTools are you using?
>
> 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.
>
My prmtop tool could add this section to any existing prmtop quite easily.
I could probably whip up something pretty quickly that will add variable 1-4
scaling to a prmtop that didn't have it before, taking as input the residue
names that needed to have a different scaling.
> 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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--
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 - 10:30:14 PDT
