Hi,
On Thu, Sep 22, 2016 at 11:21 AM, Lane Votapka <lvotapka100.gmail.com> wrote:
>
> And as for using something else to build the input structure, I was
> thinking the exact same thing. Do you know of another tool that can
> generate a PDB of an unfolded structure? I was considering just whipping
You could try using the 'makestructure' command in cpptraj to set
backbone angles to PP2 (something like 'makestructure pp2:1-X', where
X is last residue). The command doesn't do any checking for clashes
but it could be a good start. Alternatively you could try the
'permutedihedrals' command with the 'random' option which does do some
basic clash checking (see manual for more details).
-Dan
> one up myself (I already have a lot of the code to write a pdb file based
> on a z-matrix). All I need is the z-matrices of the amino acids that tleap
> uses to generate the unfolded sequence. Do you know where I could obtain
> those z-matrices?
>
> -Lane
>
> On Thu, Sep 22, 2016 at 11:17 AM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
>> 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
>> >
>> _______________________________________________
>> AMBER mailing list
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>> 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
--
-------------------------
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 Thu Sep 22 2016 - 09:00:03 PDT
