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 - 07:30:02 PST
