Hi Simon,
My example works for me in PyMOL version 1.8.0 and later. Which version do you
use?
Thomas
> On Nov 18, 2017, at 3:59 PM, Simon Kit Sang Chu <simoncks1...@gmail.com>
> wrote:
>
> Hi Thomas,
>
> Thanks for your help! But the NME and ACE are added unattached and randomly
> in the pdb. I simplified with a dipeptide AA instead. The file is attached
> here.
>
> Regards,
> Simon
>
> 2017-11-18 17:04 GMT+08:00 Thomas Holder <thomas.hol...@schrodinger.com>:
> 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 <simoncks1...@gmail.com>
> > 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.
>
>
> <peptide.pdb>
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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