I know tleap works well,
but there is a serious problem in using GLYCAM force field.
Different from Amber 10 and older version,
we can not write scee and scnb parameter value in the script for sander or pmemd in amber11,
and we have to assign it by "write14scale on" in the stage of leap.
(In detail, see 2.9.3 "Scaling of electrostatic and nonbonded interactions" in AmberTools1.5 manual)
Unfortunately, tleap can not deal with "write14scale" option...
> Don't use sleap. Use tleap.
>
>
> On Tue, Jul 5, 2011 at 12:12 PM, Tomoshi Kameda
> <kameda-tomoshi.aist.go.jp> wrote:
> > 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
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> > *********************************************
> >
> > 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Jul 05 2011 - 20:30:04 PDT
