RE: [AMBER] Amber:antechamber & heme(metal?) problems

From: Shaikh Abdul R S Ramaju <>
Date: Mon, 29 Mar 2010 14:00:11 +0800

Hi Simon Kao,

I have attached parameter files for heme. Parameters are modified based on following papers

J. Physc. Chem. B 2008, 112, 8165-8173
Proteins: Structure, Function, and Bioinformatics 62:1074-1087 (2006)

Hope it will be useful to you

Abdul Rajjak

-----Original Message-----
From: [] On Behalf Of SimonKao
Sent: Saturday, March 27, 2010 4:41 AM
Subject: [AMBER] Amber:antechamber & heme(metal?) problems

Jason and Bill, thanks for your emails!

I found the tutorial & examples of using antechamber, and I followed the steps.
But some errors happened again in antechamber.
First I separate HEM from 2dn1.pdb, as a new pdb file.
Then I attempted to run antechamber using this file with following script also shown in Amber9 manual:
> antechamber -i hem1.pdb -fi pdb -o hem1.mol2 -fo mol2 -c bcc

The error message is shown below.

Warning: the assigned bond types may be wrong, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase MAXVASTATE in define.h and recompile bondtype.C
(4) increase PSCUTOFF in define.h and recompile bondtype.C
    Be cautious, use a large value of PSCUTOFF (>10) will significantly increase the computer time
Error: cannot run "/package/chem/amber9/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in judgebondtype() of antechamber.c properly, exit

I already checked some mails in the archives, and I noticed that antechamber does not deal with metal ions.
Some replies said, I need to create the ion as a residue in leap, and provide parameters for other atom types.
Am I right?
I shall be very thankful for any more details of suggestions or comments in this regard.

Best regards,


AMBER mailing list

AMBER mailing list

Received on Sun Mar 28 2010 - 23:30:03 PDT
Custom Search