AMBER Archive (2008)

Subject: AMBER: Example .prepi file for nonstandard amino acids

From: finke_at_oakland.edu
Date: Fri May 02 2008 - 17:00:45 CDT

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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