[AMBER] residues lacking connect

From: Jorgen Simonsen <jorgen589.gmail.com>
Date: Sat, 17 Jul 2010 20:54:06 +0200


I am make parameters for a modified methionine residue - I follow the
tutorial and use their mem.lib for my protein just to observe if it works.
For the modified histidine there is no problem but I get the warning/error
at the end that

Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 -
   these don't have chain types marked:

    res total affected

which corresponds to my 3 modified MEM residues. If I try to look at the pdb
file from the prm and inpcrd

$AMBERHOME/exe/ambpdb -p nir_vac.prmtop < nir_vac.inpcrd > test.pdb

I get the residue correctly placed and no TER added to the pdb file. When I
use the desc MEM I get the following which should be the correct

 desc MEM
UNIT name:
Head atom: .R<MEM 92>.A<N 1>
Tail atom: .R<MEM 92>.A<C 5>
R<MEM 92>

How to resolve the error message?
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Received on Sat Jul 17 2010 - 12:00:04 PDT
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