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 - 07:00:04 PST
