RE: AMBER: protein-ligand complex problem

From: Ross Walker <>
Date: Thu, 10 Apr 2008 16:50:19 -0700

Dear Lynn,
I'm not entirely sure I understand your question here.
Firstly if you ran antechamber with the ligand called one thing but then changed the name of it in the pdb file before loading that into leap then the prep or mol2 file created by antechamber will not match and so leap will not recognize the ligand.
In the second case did you re-run antechamber on the LG1 ligand to generate your prep/mol2 files and frcmod files? Did you then load these into leap before loading the combined pdb? If not then that would explain why leap does not recognize it.
As for having two ligands in a complex yes you can do this. Just make sure there are ter cards between them and their coordinates do not overlap. You may need to adjust the residue numbering so they have different residue numbers although I'm not sure on this.
Good luck,

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| <> | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not be read every day, and should not be used for urgent or sensitive issues.



From: [] On Behalf Of Lynn
Sent: Thursday, April 10, 2008 15:52
Subject: AMBER: protein-ligand complex problem

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.



The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Fri Apr 18 2008 - 21:18:28 PDT
Custom Search