AMBER Archive (2009)

Subject: [AMBER] charge of Fe-heme

From: (
Date: Fri May 01 2009 - 14:08:12 CDT


In the parameter file, frcmod.hemall (/dat/contrib/heme), I find that the
total charge of the Fe-heme is -2.

When binded to Fe, the porphine are deprotonated, so the charge on porphine
should be -2. For the central Fe, both Fe(II) and Fe(III) are possible. But
only Fe(II) can bind to O2. Anyway, the total charge of Fe-heme should be 0
(Fe(II)) or +1 (Fe(III)), depending on the formal oxdation number of the
central. However, why the total charge of Fe-heme in amber force field is

Besides, I try to use antechamber to generate the partial charge for
Fe-heme. Firstly, a gaussian calculation is performed to generate the
electrostatic potential. After that, when I use the command: "antechamber -i
hem.log -fi gout -o hem.prepin -fo prepi -c resp", the following message can
be found, and the .prepin file can not be generated:

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

Can anyone give some help?


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