sorry if my reply was confusing. I did not mean to imply that I actually
use Leap to build side chains, only that it is possible. I can't give you
any examples, but if your input coordinates (such as your pdb file) have a
residue that is missing atoms compared to those in the template for that
residue, it will try to add the missing atoms according to the default
internal coordinates in the library. This is very often not what you would
want, but it will add the atoms and tell you that it did so in the output
file.
I typed in "leap add side chains" to the search feature on the Amber web
page, and there are some previous discussions that may be useful to you in
understanding the limitations of Leap for this purpose.
On Thu, Sep 13, 2018 at 3:16 AM Benjamin Clausen <s153989.student.dtu.dk>
wrote:
> Would you mind sharing how you would go about using leap to build a side
> chain?
>
> ________________________________
> Fra: Carlos Simmerling <carlos.simmerling.gmail.com>
> Sendt: 12. september 2018 18:25:16
> Til: AMBER Mailing List
> Emne: Re: [AMBER] Residue mutation and side chains
>
> Leap can build them, but it doesn't have a good way to optimize their
> rotamers prior to MD.
> I suggest using tools made for this purpose, like those in swissPDBviewer,
> or the SCWRL program. There are probably others too, and it depends on
> whether your mutations are solvent exposed (fairly easy) or buried
> (harder).
>
>
> On Wed, Sep 12, 2018 at 7:02 AM Benjamin Clausen <s153989.student.dtu.dk>
> wrote:
>
> > Hello
> >
> >
> > I am trying to carry out a residue mutation in AMBER. As far as I have
> > understood I can use "pdb4amber" to mutate residues, but the resulting
> > mutations only leave the backbone in the pdb file. Is there any way I can
> > make AMBER put in the missing side chain of the mutated residues?
> >
> > The input I have used for mutation is:
> > pdb4amber -i in.pdb -o out.pdb -m "94-GLY,94-ASP,217-GLU,217-GLN"
> >
> >
> > Best regards Benjamin
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Thu Sep 13 2018 - 09:00:02 PDT
