Thank you for your comment!
I compile AmberTools 1.5 with bugfix from 1 to 7,
and try new sleap.
However, sleap aborts yet....
Tomoshi Kameda
> For now, we recommend you use tleap from a fully patched AmberTools
> 1.5. Please let us know if that doesn't work.
>
>
> On Tue, Jul 5, 2011 at 2:09 AM, Tomoshi Kameda
> <kameda-tomoshi.aist.go.jp> wrote:
> > In AmberTools1.4 manual,
> >
> >> 3.5.2.1 Example: Building a lipid with LEaP.
> >>
> >> One need not load the main GLYCAM prep files in order to build a lipid using the
> >> GLYCAM 06 parameter set, but it is automatically loaded with the default
> >> leaprc.GLYCAM_06. Note that the lipid generated by this set of commands is not necessarily
> >> aligned appropriately to create a bilayer along an axis. The commands to use are:
> >>
> >> source leaprc.GLYCAM_06 # source the leaprc for GLYCAM 06
> >> loadamberprep GLYCAM_06_lipids.prep # load the lipid prep file
> >> set CHO tail CHO.1.C5 # set the tail atom of CHO as C5.
> >> set PGL head PGL.1.O1 # set the head atom of PGL to O1
> >> set PGL tail PGL.1.C3 # set the tail atom of PGL to C3
> >> lipid = sequence { CHO PGL MYR } # generate the straight-chain
> >> # portion of the lipid
> >> set lipid tail lipid.2.C2 # set the tail atom of PGL to C2
> >> lipid = sequence { lipid MY2 } # add MY2 to the "lipid" unit
> >> impose lipid {2 3} { {C1 C2 C3 O1 163} } # set torsions for
> >> impose lipid {2 3} { {C2 C3 O1 C1 -180} } # PGL & MYR
> >> impose lipid {2 3} { {C3 O1 C1 C2 180} }
> >> impose lipid {2 4} { {O4 C1 C2 O1 -60} } # set torsions for
> >> impose lipid {2 4} { {C1 C2 O1 C1 -180} } # PGL & MY2
> >> impose lipid {2 4} { {C2 O1 C1 C2 180} }
> >> # Note that the values here may not necessarily
> >> # reflect the best choice of torsions.
> >> savepdb lipid DMPC.pdb # save pdb file
> >> saveamberparm lipid DMPC.top DMPC.crd # save top and crd files
> >
> > tleap can read upper contents, and produces proper output such as DMPC.top.
> > However, sleap aborts with error message:
> >> [gtkleap]$ loadamberprep GLYCAM_06_lipids.prep
> >> [gtkleap]$ set CHO tail CHO.1.C5
> >> [gtkleap]$ set PGL head PGL.1.O1
> >> sleap: ../freelib/boost/shared_ptr.hpp:247: boost::detail::shared_ptr_traits<T>::reference boost::shared_ptr ? ? ? ? ? <T>::operator*() const [with T = mort::root_t]: Assertion `px != 0' failed.
> >
> > So, I'm going to know whether sleap can deal with lipids or not.
> >
> >
> > Thanks
> >
> > Tomoshi Kameda
> >
> >
> > *********************************************
> >
> > Tomoshi Kameda, Ph.D.
> >
> > Computational Biology Research Center(CBRC),
> > National Institute of Advanced Industrial Science and Technology(AIST)
> >
> > AIST Tokyo Waterfront Bio-IT research Building,
> > 2-4-7 Aomi, Koto, Tokyo, Japan 135-0064
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
> _______________________________________________
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*********************************************
Tomoshi Kameda, Ph.D.
Computational Biology Research Center(CBRC),
National Institute of Advanced Industrial Science and Technology(AIST)
AIST Tokyo Waterfront Bio-IT research Building,
2-4-7 Aomi, Koto, Tokyo, Japan 135-0064
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Received on Tue Jul 05 2011 - 09:30:04 PDT
