If those are your commands, all of your alanines are NALA because you're
explicitly classifying them as such. Change NALA -> ALA in your sequence
and that should fix it.
Best,
Cory
On Sun, Jan 5, 2020 at 4:03 PM ankita mehta <mehtaroadies.gmail.com> wrote:
> Hiii David,
> these are my tleap commands:
> source leaprc.ff99SB
> source leaprc.gaff
> 1bnr = sequence {NALA GLN VAL ILE ASN THR PHE ASP GLY VAL NALA ASP TYR LEU
> GLN THR TYR HIS LYS LEU PRO ASP ASN TYR ILE THR LYS SER GLU NALA GLN NALA
> LEU GLY TRP VAL NALA SER LYS GLY ASN LEU NALA ASP VAL NALA PRO GLY LYS SER
> ILE GLY GLY ASP ILE PHE SER ASN ARG GLU GLY LYS LEU PRO GLY LYS SER GLY ARG
> THR TRP ARG GLU NALA ASP ILE ASN TYR THR SER GLY PHE ARG ASN SER ASP ARG
> ILE LEU TYR SER SER ASP TRP LEU ILE TYR LYS THR THR ASP HIS TYR GLN THR PHE
> THR LYS ILE CARG}
> saveoff 1bnr 1bnr_linear.lib
> saveoff 1bnr 1bnr_linear.pdb
> loadoff 1bnr 1bnr_linear.lib
> saveamberparm 1bnr 1bnr_linear.prmtop 1bnr_linear.0.inpcrd
> quit
> ~i intend to build a linear structure of these residues...
> my output is :
> attached below:
> thanks
>
>
>
>
>
>
> On Mon, Jan 6, 2020 at 12:03 AM David Case <david.case.rutgers.edu> wrote:
>
> > On Sun, Jan 05, 2020, ankita mehta wrote:
> >
> > > what is the solution to remove TER inserted before ALA?
> > >It cinsiders all alanine to be NALA?
> >
> > Just to repeat: we have no idea what sequence (or other commands) you
> > used. It is generally far better to tell us what you actually did, not
> > what your intent was. That is, don't say "I'm trying to build a pdb file
> > through sequence command" (that describes your intent); rather say "here
> > are the exact commands I gave to tleap, and here was the result." (that
> > describes what you actually did.)
> >
> > In this particular case, as Carlos has noted, the structures Amber
> > creates by default are not intended to be realisitic configurations.
> >
> > ....dac
> >
> >
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> >
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>
--
Cory M. Ayres, PhD
BMB Chief Adjudicator of Laboratory Safety
Postdoctoral Research Associate
University of Notre Dame
Department of Chemistry and Biochemistry
Harper Cancer Research Institute
A221 Harper Hall
1234 Notre Dame Avenue
South Bend, IN 46617
cayres.nd.edu
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Received on Sun Jan 05 2020 - 20:30:02 PST
