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
>>
>> _______________________________________________
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>> 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
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Received on Tue Jul 05 2011 - 10:30:03 PDT
