Hi Daniel,
Thanks for your suggestions.
I installed AmberTools16, but the segfault still occurred in the same way
as before. I also tried your suggestion to remove the "combine" command,
just using mol_0. Still no luck. The segfault still occurs upon the
"sequence" command.
Best,
-Lane
On Wed, Sep 21, 2016 at 8:12 PM, Daniel Roe <daniel.r.roe.gmail.com> 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
>
>
>
> --
> -------------------------
> 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
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Received on Thu Sep 22 2016 - 08:30:02 PDT
