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
-o ANTECHAMBER_BOND_TYPE.AC -f ac -j full
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
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full"
in judgebondtype() of antechamber.c properly, exit
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Received on Fri Apr 18 2008 - 21:13:39 PDT
