Hi,
On Wed, Feb 5, 2020 at 2:10 PM ankita mehta <mehtaroadies.gmail.com> wrote:
>
> pdb4amber command can do the purpose?
> Cannot do manualy each time?
> Need to embed in code.
The -y / --nohyd command line options for pdb4amber will strip away
hydrogen atoms. This information is available in the manual entry (and
the help text) for pdb4amber.
In future emails, you may get more responses if you use a subject that
generally describes the issue you are having (I see "hiii" and assume
it's spam)...
-Dan
>
>
> On Thu 6 Feb, 2020, 12:30 AM ankita mehta, <mehtaroadies.gmail.com> wrote:
>
> > Is it for
> > 1. N terminal alanine residue or
> > 2.Any N terminal residue
> > 2. Rest of Alanines in file(IF they were present) or
> > 3.all the other amino acids
> >
> >
> > shouldn't have Hydrogen in it?
> >
> > On Thu 6 Feb, 2020, 12:16 AM David A Case, <david.case.rutgers.edu> wrote:
> >
> >> On Wed, Feb 05, 2020, ankita mehta wrote:
> >>
> >> >i wanted to generate prmtop and inpcrd files of attached pdb.
> >> >But , it is giving me errors.
> >>
> >> If you haven't yet done so, do a Google search on Amber "does not have a
> >> type". You'll get the general idea.
> >>
> >> Your pdb file has a N-terminal alanine with an H atom in it. But the
> >> Amber library for alanine in an Nterminal position uses H1/H2/H3, but no
> >> H.
> >>
> >> Simplest solution is to remove the H atom from the pdb file: tleap will
> >> build in the H1/H2/H3 for you.
> >>
> >> ....dac
> >>
> >>
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> >>
> >
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Received on Thu Feb 06 2020 - 05:30:02 PST
