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
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Received on Wed Sep 21 2016 - 17:30:02 PDT
