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
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Received on Mon Jul 04 2011 - 23:30:03 PDT
