Hello:
I have made a mutation in position 1 of a peptide chain (by stripping out
the side chain and adding my new amino acid which I have parameters for) to
an unnatural amino acid.
The unnatural amino acid was built using residuegen and I am building
everything using xleap.
Upon looking at the structure, I noticed that my N-terminus has only 1
hydrogen instead of the usual 3. It is my understanding that in the natural
amino acids a residue at the N-terminus (i.e. Ala) will be replaced by a
NAla, which will have the proper valence for the N-terminus.
I have tried several different things including changing my prep file from
OMIT to NOMIT so that the beginning dummy atoms are not omitted, but that
did not seem to work.
Is it possible to do something similar for my unnatural amino acid to what
is done for the natural amino acids in AMBER? If so, could someone tell me
what I could do to proceed? Thanks in advance for your help and have a good
day.
Best,
George
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Received on Tue Sep 06 2011 - 07:30:03 PDT
