AMBER Archive (2009)

Subject: [AMBER] creating new residue adds none wanted ter

From: Jorgen Simonsen (jorgen589_at_gmail.com)
Date: Mon May 04 2009 - 02:49:47 CDT

Hi,

I am trying to create a new residues following the tutorial "*Simulating a
Solvated Protein that Contains Non-Standard Residues" *where I also have MET
residue that I have changed to MEM adding an ion to the residue. The problem
is that when I use ambertool it add a TER to my residue although it is
within a sequence in the protein and should not have added the TER.

If i load the file and display
desc MEM

it returns

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

if I do it on the MET residue
UNIT name: MET
Head atom: .R<MET 1>.A<N 1>
Tail atom: .R<MET 1>.A<C 16>
Contents:
R<MET 1>

I can see the numbering is different but if I then reorder so the C/O are
number five in the pdb it still adds the TER to the residue. If I use the
LIB file from the tutorial on MEM it also displays 1 and 5.

Any hint on how to fix the problem - thanks in advance

Best regards

Jorgen
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