AMBER group,
We are trying to build a o-nitrotyrosine aminoacid using antechamber. This nitrotyrosine is intended to be incorporated into a peptide just as any normal amino acid would.
However, the connectivities produced from a PDB of nitrotyrosine (created in SPARTAN) end up being incorrect. Our attempts to modify a normal tyrosine prepi file have also ended in problems. (Our tyrosine prepi file works well but once we change it, problems occur).
I think the problem is getting the connectivities right in the prepi file. Something which would help would be a sample prepi file for a modified tyrosine with the o- position substitued with "something". Then would could just add the extra N O O atoms in place of whatever is there.
Does anyone have such a file or know where a sample can be found on the web?
Thanks.
John Finke
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Received on Sun May 04 2008 - 06:07:46 PDT
