AMBER Archive (2009)

Subject: [AMBER] Unknown residue: MOL number: 30 type: Terminal/last

From: Workalemhu Berhanu (
Date: Mon Jun 08 2009 - 13:30:43 CDT

Dear amber users
I am new user of amber. I created my ligand and peptide complex using PatchDock (Nucl. Acids. Res. 33: W363-367, 2005). When I used tleap for my ligand and peptide complex (which I named as solution.pdb) I got the errors shown below. I am try to study the effect of small organic molecules on breaking of beak sheet . I have attached the pdb file of the complex I got after docking. My peptide is obtained from protein data bank and I used antechamber for GAFF for my organic molecule. Could some help me in figuring out what is wrong with my approach?
Thank you
With regards
COM =loadpdb "solution.pdb"
Loading PDB file: ./solution.pdb
 (starting new molecule for chain B)
 (starting new molecule for chain D)
 (starting new molecule for chain )
Unknown residue: MOL number: 30 type: Terminal/last
..relaxing end constraints to try for a dbase match
  -no luck
  total atoms in file: 158
  Leap added 188 missing atoms according to residue templates:
       188 H / lone pairs
check COM
Checking 'COM'....
Warning: Close contact of 1.391742 angstroms between .R<CVAL 6>.A<HG23 14> and .R<VAL 14>.A<HG11 8>
Checking parameters for unit 'COM'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 1
Unit is OK.
When I typed edit COM I can only see the peptide and my ligand is missing

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