Shahrokh Safarian wrote:
Dear colleague
I did have a try for molecular modeling of a metaloenzyme using Gromacs
3.3.1. But during establishment of the related topology file, an error
about introducing of the iron atom was appeared. As you know,
recommendatin of the iron atom into the program has been performed in
the structure of the heme group. So, I did have many tries to change the
ffG43a1.rtp and ffG43a1.atp to recomend Fe2+ into the program. After
that, the calculation was proceeded but missnig of some atoms in the
established pdb file was happened. Could you please inform me about the
adding a new atom type (Fe2+)way for introducing of a new atom type (specially Fe2+) into Gromacs.
This is a specialist topic, and should not be attempted by anyone new to
GROMACS and/or MD simulation. Your atoms missing from the pdb file
probably have nothing to do with your heme group, but you should have
told us whether they did. You will probably need to edit specbond.dat
(http://wiki.gromacs.org/index.php/specbond.dat) to make the bonded
links appropriately. Otherwise, read and consult chapter five of the
manual very closely.
Mark
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