If you use AmberTools 1.5, fully patched, tleap will automatically
write scaling information into the topology file. You do not need to
use the command "write14scale"; tleap will always write this
information. But, you must use a fully updated version of AmberTools
1.5 to get this functionality.
2011/7/5 Tomoshi Kameda <kameda-tomoshi.aist.go.jp>:
> 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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:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Wed Jul 06 2011 - 07:30:03 PDT
