AMBER Archive (2008)

Subject: AMBER: protein-ligand complex problem

From: Lynn (
Date: Thu Apr 10 2008 - 17:51:32 CDT

Dear all:

I am trying MD with a protein-ligand complex, the ligand is 4OH-Tamoxifen.

If I use default "OHT" as the ligand's name, both the antechamber and leap
process is ok. However, I changed the name of the ligand before leap-- row
18-20 in the pdb file. The antechamber is ok, but in the leap ,when i load
the complex, it says something wrong, error.says:
Created a new atom named: NE2 within residue: .R<GLH 71>
  Added missing heavy atom: .R<GLH 71>.A<OE2 13>
If I "check", it exports FATAL error. First I thought it maybe the
protonated problem( but i use "OHT" as residue name in pdb file, there is no
such warning). But I changed GLN71 to GLH71, the error still exist.

Why such strange thing happen?
Another question: Can I set two same ligand in a complex, and run MD?(the
X-ray structure already exist). If positive, how to set the ligand's residue
name in the pdb file?

The attached 2Fmo1.pdb run well ,but 2Fmo2.pdb did not.



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