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
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Received on Wed Sep 21 2016 - 17:30:03 PDT
