AMBER Archive (2008)

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

From: finke_at_oakland.edu
Date: Fri May 02 2008 - 20:06:30 CDT

David,

Thanks. + follow up question.

One problem we have had is that our side chain atoms are the one's bonded to the
previous amino acid and/or following amino acid.

Is there a way to designate main chain N, CA, C atoms in the mol2 file? These are
designated by M in the prepi files.

Thanks again,

John Finke


attached mail follows:

On Fri, May 02, 2008, finke_at_oakland.edu wrote:

> 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 suggest you use mol2 files, that are much simpler to work with than prepi
files. (We are trying to deprecate that file format anyway).

In mol2 files, you just have a list of bonds, making it easy to examine and
modify connectivities, etc.

...good luck...dac

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