Hi Simon,
I think this is the code you're looking for:
from pymol import cmd, editor
cmd.set('retain_order', 0)
cmd.fab('APAPAPAP')
editor.attach_amino_acid("last name C", 'nme')
editor.attach_amino_acid("first name N", 'ace')
Hope that helps.
Cheers,
Thomas
> On Nov 17, 2017, at 8:26 AM, Simon Kit Sang Chu <[email protected]>
> wrote:
>
> Hi everyone,
>
> I am generating segments of peptide to be used in GROMACS. I might be using
> amber which does not allow automatic capping. Therefore, I hope to solve it
> with Pymol.
>
> Currently, I use a pml scipt to generate the pdb file automatically. The
> script is simple.
>
> for aa in "APAPAPAP" : cmd._alt(string.lower(aa))
> cmd.save("peptide.pdb")
>
> However, if I want to add NME and ACE caps, is there any residue code
> available? Like XAPAPAPAPY where X and Y are NME and ACE? The main point is
> to automize the process since I don't want to write NME / ACE manually
> everytime.
>
> I appreciate any suggestion and comment.
>
> Regards,
> Simon
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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