AMBER Archive (2005)

Subject: AMBER: missing residue

From: xueping (xueping22_at_yahoo.com)
Date: Mon Mar 28 2005 - 01:34:17 CST

Dear all,

I have a protein with a first missing residue,
Methionine. I added the residue using Hyperchem and
load in xleap, when i check the unit, it gives me the
following message,
 
WARNING: There is a bond of 75.141750 angstroms
between:
------- .R<NMET 1>.A<C 18> and .R<ALA 2>.A<N 1>

This is due to the MET that i have added to the second
residue, ALA. I know that warning for close contact
can be ignored since minimization will be carried out.
But in this case, the residue is 75.141750 angstrom
away from the second residue, i wonder whether my
starting structure is correct, because minimization
will not change the structure drastically.

Thanks in advance.

Regards
xueping

                
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