the structure might not be very relevant, but I've found that structures
built in this way typically respond fine to minimization and MD. It might
still be a good idea to use other methods to build input structures, since
they would let you use a pdb input file and not crash the routine that
builds structure from sequence.
carlos
On Thu, Sep 22, 2016 at 11:14 AM, Lane Votapka <lvotapka100.gmail.com>
wrote:
> Hi Bill,
>
> Thanks for your suggestion, but I'm afraid that running on OSX won't be
> useful for my particular situation. I need to be able to run tleap on Linux
> for the task I'm trying to accomplish.
>
> Yes, I realize that the structure generated by "sequence" will not be
> physically realistic, but that's on purpose. I'm trying to generate a
> completely unfolded structure and I run minimizations before starting any
> sort of simulations. I guess it's understandable though that the bug has
> gone unnoticed before now.
>
> Do you guys think that I can expect the bug to be addressed anytime soon,
> or should I look for other solutions to this problem beyond tleap?
>
> -Lane
>
> On Wed, Sep 21, 2016 at 8:34 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> > With the amber14 release of leap, it didn't coredump on OSX for me.
> >
> > You realize your structure is meaningless even if you can generate it,
> > and will likely crash any program you feed it to, because 'sequence'
> > does no steric checking or adjustment as it tacks residues together.
> > That's why the bug you have likely found hasn't been seen before.
> >
> > Bill
> >
> >
> > On 9/21/16 5:12 PM, Daniel Roe wrote:
> > > Also, the command
> > >
> > >> sys = combine { mol_0 }
> > > seems redundant if you're not actually combining it with anything. Try
> > > just using mol_0; see if that helps.
> > >
> > > -Dan
> > >
> > > On Wed, Sep 21, 2016 at 8:11 PM, Daniel Roe <daniel.r.roe.gmail.com>
> > wrote:
> > >> Hi,
> > >>
> > >> Have you tried tleap from AmberTools 16?
> > >>
> > >> -Dan
> > >>
> > >> On Wed, Sep 21, 2016 at 4:31 PM, Lane Votapka <lvotapka100.gmail.com>
> > wrote:
> > >>> Hi AMBER developers and users,
> > >>>
> > >>> When I run the following leaprc in the tleap that comes with Amber14,
> > the
> > >>> program fails in a segfault:
> > >>>
> > >>> set default PBradii mbondi3
> > >>> source leaprc.ff14SBonlysc
> > >>> source leaprc.gaff
> > >>> mol_0 = sequence { NMET THR HIE GLN THR HIE ALA TYR HIE MET VAL ASN
> > PRO SER
> > >>> PRO TRP PRO LEU THR GLY ALA LEU SER ALA LEU LEU MET THR SER GLY LEU
> > THR MET
> > >>> TRP PHE HIE PHE ASN SER MET THR LEU LEU MET ILE GLY LEU THR THR ASN
> > MET LEU
> > >>> THR MET TYR GLN TRP TRP ARG ASP VAL ILE ARG GLU SER THR PHE GLN GLY
> > HIE HIE
> > >>> THR PRO ALA VAL GLN LYS GLY LEU ARG TYR GLY MET ILE LEU PHE ILE ILE
> > SER GLU
> > >>> VAL LEU PHE PHE THR GLY PHE PHE TRP ALA PHE TYR HIE SER SER LEU ALA
> > PRO THR
> > >>> PRO GLU LEU GLY GLY CYS TRP PRO PRO THR GLY ILE HIE PRO LEU ASN PRO
> > LEU GLU
> > >>> VAL PRO LEU LEU ASN THR SER VAL LEU LEU ALA SER GLY VAL SER ILE THR
> > TRP ALA
> > >>> HIE HIE SER LEU MET GLU GLY ASP ARG LYS HIE MET LEU GLN ALA LEU PHE
> > ILE THR
> > >>> ILE THR LEU GLY VAL TYR PHE THR LEU LEU GLN ALA SER GLU TYR TYR GLU
> > ALA PRO
> > >>> PHE THR ILE SER ASP GLY VAL TYR GLY SER THR PHE PHE VAL ALA THR GLY
> > PHE HIE
> > >>> GLY LEU HIE VAL ILE ILE GLY SER THR PHE LEU ILE VAL CYS PHE PHE ARG
> > GLN LEU
> > >>> LYS PHE HIE PHE THR SER ASN HIE HIE PHE GLY PHE GLU ALA GLY ALA TRP
> > TYR TRP
> > >>> HIE PHE VAL ASP VAL VAL TRP LEU PHE LEU TYR VAL SER ILE TYR TRP TRP
> GLY
> > >>> CSER }
> > >>>
> > >>> translate mol_0 { 0.0 0.0 0.0 }
> > >>> sys = combine { mol_0 }
> > >>> check sys
> > >>> saveAmberParm sys system.top system.mdcrd
> > >>> quit
> > >>>
> > >>> The output says:
> > >>>
> > >>> ERROR: syntax error
> > >>> Segmentation fault (core dumped)
> > >>>
> > >>> If I enter the commands one by one, the segfault occurs on the
> > "sequence"
> > >>> command.
> > >>>
> > >>> If I change the sequence, but keep it the same length, the error
> still
> > >>> occurs. If I shorten the sequence, the segfault does not occur. I can
> > even
> > >>> use a long sequence of alanines and the segfault still happens.
> > >>>
> > >>> This makes me think that there is a memory overflow or something with
> > >>> longer entries to the "sequence" command in the tleap code.
> > >>>
> > >>> Best,
> > >>> -Lane
> > >>>
> > >>> --
> > >>> Lane Votapka Ph.D.
> > >>> Postdoctoral Associate, Dill Laboratory 115G
> > >>> Laufer Center for Physical and Quantitative Biology
> > >>> Stony Brook University
> > >>> Stony Brook, NY 11794
> > >>> _______________________________________________
> > >>> AMBER mailing list
> > >>> AMBER.ambermd.org
> > >>> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >>
> > >> --
> > >> -------------------------
> > >> Daniel R. Roe
> > >> Laboratory of Computational Biology
> > >> National Institutes of Health, NHLBI
> > >> 5635 Fishers Ln, Rm T900
> > >> Rockville MD, 20852
> > >> https://www.lobos.nih.gov/lcb
> > >
> > >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Lane Votapka Ph.D.
> Postdoctoral Associate, Dill Laboratory 115G
> Laufer Center for Physical and Quantitative Biology
> Stony Brook University
> Stony Brook, NY 11794
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Sep 22 2016 - 08:30:03 PDT
