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
Received on Thu Sep 22 2016 - 08:30:03 PDT
