[gmx-users] adding a new atom type (Fe2+)

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jun 5 03:59:21 CEST 2007

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.


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