AMBER Archive (2008)

Subject: AMBER: RE: Force Field Parameterizing

From: Shultz, Jack (
Date: Mon Mar 24 2008 - 10:31:32 CDT

I'm looking at the H-Cluster for Fe-Hydrogenase, trying to generate a topology file. Xleap does not have bond parameters for Iron. So I tried to generate the parameters using antechamber and got these error messages. In order to find parameters should I harvest from literature or is there another way to generate the parameters I'm seeking.

I understand these transition metals present theoretical problems with their complicated orbitals. Is Amber well suited for this type of problem?

$ $AMBERHOME/exe/antechamber -i 2Fe2S.mol2 -fi mol2 -o 2Fe2S.prepin
-fo prepi -c bcc -s 2
Running: /usr/local/amber9/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0

For atom[3]:Fe1, the best APS is not zero, exit
For atom[6]:Fe2, the best APS is not zero, exit
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 "/usr/local/amber9/exe/bondtype -i
in judgebondtype() of antechamber.c properly, exit
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