normal How to build CG structure if I have X AA

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7 years 7 months ago #5854 by elkafirmanda
How to build CG structure if I have X AA was created by elkafirmanda
Hi, I just got "X" amino acids on DSSP, what does it means ? when I use the DSSP file to build coarse grained structure with martini 2.2 force field, I lost some amino acids because of this "x" amino acids on DSSP. So, how to build CG structure if I have this "x" amino acids ? I want to build CG structure for phycocyanin (1GH0) chain A-F. As far as I know, the "x" amino acids refers to modified residues called "MEN", L-Peptide Linking. Thank you for your help.

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7 years 5 months ago #6011 by peterkroon
Replied by peterkroon on topic How to build CG structure if I have X AA
Hi,

if these X aminoacids are different enough to change the behaviour of your protein in a way that you'll observe you'll need to figure out how to describe these in Martini and add them to Martinize. If DSSP doesn't want to cooperate you can also feed its (modified) output to martinize by hand using the -ss flag (check martinize.py --help)

Peter

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