what is the solution to remove TER inserted before ALA?
It cinsiders all alanine to be NALA?
How that works?
On Sun 5 Jan, 2020, 9:01 PM Carlos Simmerling, <carlos.simmerling.gmail.com>
wrote:
> The sequence command builds a linear structure. Leap makes no attempt to
> model a reasonable structure. You would need other tools for that, such as
> Rosetta or Modeler.
>
> On Sun, Jan 5, 2020, 10:21 AM ankita mehta <mehtaroadies.gmail.com> wrote:
>
> > I m trying to build a pdb file through sequence command, whose fasta
> format
> > file i m providing.
> > When i see the generated pdb file, i recognized my all ALA to be NALA and
> > inserted TER exactly before ALA.
> > then i am doing minimization two different runs, one is without box and
> > one is big box.. That too is showing me errors.
> > But i guess initial trouble is to fix TER residues before ALA.
> >
> > Can u pls explain on what principles does sequence command generate
> > coordinates?
> >
> > Thanks
> >
> >
> >
> > On Sun 5 Jan, 2020, 8:03 PM Carlos Simmerling, <
> > carlos.simmerling.gmail.com>
> > wrote:
> >
> > > Maybe you could try to briefly explain what you're trying to do...
> There
> > > are many options and it's hard to offer advice on steps if we don't
> know
> > > what they are meant to accomplish
> > >
> > > On Sun, Jan 5, 2020, 9:19 AM ankita mehta <mehtaroadies.gmail.com>
> > wrote:
> > >
> > > > Hiii
> > > > Attached are my files.two perl scripts for two different runs. And
> > fasta
> > > > file for sequence..
> > > > Exactly pdb file generated through tleap had TER before ALA.
> > > > Moreover ALA had hydrogens in it.. See the attached screen shots and
> > > files.
> > > > Pls suggest how to deal with this..
> > > >
> > > >
> > > > On Sun 5 Jan, 2020, 7:18 PM David Case, <david.case.rutgers.edu>
> > wrote:
> > > >
> > > > > On Sun, Jan 05, 2020, ankita mehta wrote:
> > > > >
> > > > > >Why tleap is considering all ALANINE to be NALA?
> > > > >
> > > > > We have so little information about what you did, and what pdb file
> > you
> > > > > loaded, to offer any useful information. You apparently used a
> > > sequence
> > > > > command, but we don't have any information about what step that
> was,
> > or
> > > > > what was in it.
> > > > >
> > > > > Generally, the default in tleap is to make change an N-terminal ALA
> > > > > residue to NALA. Note that NALA (and other N-terminal residues)
> does
> > > > > not have an "H" atom in it. Do you have any unwanted TER cards in
> > you
> > > > > PDB file right before the ALA residues?
> > > > >
> > > > > ....dac
> > > > >
> > > > >
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Received on Sun Jan 05 2020 - 08:00:02 PST
