[gmx-users] topology for iron dicitrate

syma syma.khalid at bioch.ox.ac.uk
Wed Mar 29 22:17:10 CEST 2006


Please can anyone advise me on the best way to make a gromos96 topology for
iron dicitrate?

The coordinates I want to use are attached. I originally tried usng the
prodrg beta server. So each citrate ligand was defined as a separate
molecule with the FeIII ions held in place by non bonded interactions only.
When minimising in gmx the FeIII ions 'flew off', so I'm thinking it would
be best to make a topology for the whole complex as one ligand. I would be
happy to restrain bonds involving the Fe ions.

Help with this would be hugely appreciated.



Dr Syma Khalid                                  
Department of Biochemistry,       
University of Oxford                       
South Parks Road,


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