AMBER Archive (2009)

Subject: AMBER: ligand parameter

From: Bo Baker (
Date: Mon Jan 05 2009 - 16:05:18 CST

Dear Amber:

I try to build amberparm with my target protein and the ligands. I used
antechamber to build the prep and parm for each ligands, and loaded them
together with .ff99. When I try to save amberparm, the program complains

WARNING: There is a bond of 16.699220 angstroms between:
------- .R<FAD 621>.A<C4A 53> and .R<FMN 622>.A<O4 1>
WARNING: There is a bond of 16.116888 angstroms between:
------- .R<FAD 621>.A<N3A 52> and .R<FAD 621>.A<C4A 53>
WARNING: There is a bond of 16.770245 angstroms between:
------- .R<FAD 621>.A<C5A 47> and .R<FAD 621>.A<C6A 48>
WARNING: There is a bond of 14.378186 angstroms between:
------- .R<FAD 621>.A<N7A 46> and .R<FAD 621>.A<C5A 47>
WARNING: There is a bond of 13.779173 angstroms between:
------- .R<FAD 621>.A<C4A 8> and .R<FAD 621>.A<N9A 44>
WARNING: There is a bond of 23.963962 angstroms between:
------- .R<FMN 622>.A<O1P 31> and .R<NAP 623>.A<NO1 1>

I add "TER" at the end of each ligand in protein pdb file. I don't
understand why there are bonds among these ligands. I guess that the parm
files are not generated properly. I use Amber7.

I have the ligand files attached.

Thank you for your advice


  • application/octet-stream attachment: NAPa.parm

  • application/octet-stream attachment: NAPa.prep
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