I will try fixing it.
But I read sequence command format from
https://ambermd.org/tutorials/basic/tutorial3/section1.htm
Thanks1
On Mon, Jan 6, 2020 at 9:49 AM Cory Ayres <cayres.nd.edu> wrote:
> 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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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> 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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>
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Received on Mon Jan 06 2020 - 00:00:02 PST
