Hello-- > > I would like to calculate the structure of a protein of which > N-terminal end is PCA (pyroglutamic acid). Does anyone know how to > edit XXX.pro and XXX.par files to define this non-standard amino > acid, PCA?
As you found, PCA is not included in Xplor-NIH's distributed
topology/parameters. To obtain something which will likely work for
you I did this:
1) from the Xplor-NIH FAQ,
https://nmr.cit.nih.gov/xplor-nih/faq.html#node0150.txt
I found the like for the PDB Pigand Expo
http://ligand-expo.rcsb.org/
2) There I searched up PCA, and grabbed the download:
Component definition in mmCIF format
3) I ran eginput/PSF_generation/genLigandCif.py from the Xplor-NIH
distribution:
./genLigandCif.py PCA
which generated .top and .par files. These I edited to remove the
C-terminal OH group, and added back the bond, angle and improper
parameters required for linking to the next residue. I have
attached the modified .top and .par files.
4) I have also included a short generation script, which shows how
these files might be used in a script. Here, I test the top/par
files by generating and writing out a two residue peptide with
sequence "PCA ALA"
Please let me know if you have questions.
Charles
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PCA.top
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PCA.par
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gen.py
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