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
Received on Tue Jul 05 2011 - 07:30:04 PDT
