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mutate residue at termini

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mutate residue at termini

interface design is changing a terminal aminoacid in my complex and
I would like to mutate it back to wildtype using the MutateResidue
mover, but every time I try to do that for the N or C terminus I get
segmentation fault. This is system independant, I see this for every complex I work with.
Is there a way around it, without going back to the interface design ?



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Fri, 2013-09-13 09:24

The problem is that you're not providing the appropriate residue type name. The issue is that terminal residue types are "patched" to add the appropriate atoms for the terminal behavior. Take a look at the output PDBs, specifically the energy table at the end. Notice that the names of the terminal residues aren't just "ALA", but are "ALA_p:NtermProteinFull" or "ALA_p:CtermProteinFull". the "_p:" means it's a patched residue type, and the "NtermProteinFull" and "CtermProteinFull" are the patch types applied to the residue. The full string, with the patch designator and patch type string is what you need to give to the new_res parameter of MutateResidue.

That said, the fact that you're getting a segmentation fault is a bug. At the very least it should be giving you a (hopefully helpful) error message.

Fri, 2013-09-13 10:55

Hi Thanks for quick reply.
It works great now!


Mon, 2013-09-16 08:08