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 *X*APAPAPAP*Y* 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
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