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terminus capping

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terminus capping
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Does anyone know if it is possible to incorporate acetylation (Ac-) at the N-terminus and amidation (-NH2) at the C-terminus when doing a docking run? In my starting PDB file, these atoms are listed as HETATM and when I run dock, the output files no longer have the HETATM atoms. I have a case where the presence of these termini caps make a difference in experimental binding and would like to take a look at it using RosettaDock.

Wed, 2009-10-07 11:16
mbellows

> Does anyone know if it is possible to incorporate acetylation (Ac-) at the N-terminus and amidation (-NH2) at the C-terminus when doing a docking run? In my starting PDB file, these atoms are listed as HETATM and when I run dock, the output files no longer have the HETATM atoms. I have a case where the presence of these termini caps make a difference in experimental binding and would like to take a look at it using RosettaDock.

Hi,
I had the same question. Rosetta would give error saying unrecognized residue. I guess, there is no direct/simpler way to include these (based on my email conversation with the developers). Please let me know if you are able to make progress along these lines.

Regards,
Mohan

Fri, 2010-08-06 22:30
mboggara