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
Description: Protein Databank data
------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net