Adding ACE-NME caps to an AMBER structure
Open the original PRMTOP and PDB files in VMD. Use the pdbter plugin to generate a PDB, and open it in a text editor. Follow these steps for each molecular fragment to be capped.
© Toni Giorgino, 2010
ACE at N-terminus
- go at the N-terminus and find the first H2 atom
- change its name into C, its resname into ACE, and its residue number
- remove H2, H3
Adding NME at C-terminus
- go at the C-terminus and find the terminal oxygen (OXT)
- change its name and residue into N-NME; change its residue number
Done
Now process the resulting PDB with tleap. Note that residue and atom numbers will be different from the original structure.
License
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