AMBER Archive (2003)

Subject: Re: AMBER: no defined type for atom N atom

From: David A. Case (case_at_scripps.edu)
Date: Fri Sep 19 2003 - 12:01:29 CDT

On Fri, Sep 19, 2003, Wu Yingliang wrote:
>
>
> I have a short peptide (about 30 residues) aminated in the C terminal. When
> I load it in xleap program, it tells me: there is no defined type for heavy
> atom N. In order to produce corresponding topology and coordinate file, I
> have to delete it, and atom OXT was then added.

You will need to define a residue (with some special name) that matches the
chemistry of your C-terminal residue. It's probably easiest to start with
the current c-terminal residue for the side chain you have, and modify it,
using xleap.

This is not the simplest process, but if you are patient, and pay close
attention to warnings and errors that leap may give you, you should succeed.

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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