[gmx-users] Handling terminal amino acids for Amber

D. Yousefi da.yousefi at gmail.com
Sat Mar 2 09:31:24 CET 2019


According to the output for "gmx help pdb2gmx",

    "Default termini are ionized (NH3+ and COO-), respectively.  ... The
AMBER force fields have unique forms for the terminal residues, and these
are incompatible with the -ter mechanism. You need to prefix your N- or
C-terminal residue names with "N" or "C" respectively"

I'm using AMBER99SB. So, for example, I have to change the residue name for
my N-terminal leucine from LEU to NLEU. Is it right? I'm in doubt because
this would make my pdb non-standard. Indeed, the visualization becomes
messy in PyMOL after this change.

Moreover, I need to use the noter option for pdb2gmx, am I right?

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