[gmx-users] heme topology

[Marc Ceruso]

On Sat, 22 Jun 2002, Valentin Gogonea wrote:

> Hello gromacs users,
> 
> I have a question about how pdb2gmx creates topology for His-Heme group. 
> It seems to me that in the .rtp file a bond of type Fe-N(His) is not 
> defined for HEME residue, still pdb2gmx creates one. Can anybody explain 
> me how this is done? Does pdb2gmx checks for proximity of atoms based on 
> distance and uses ffgmxbon.itp file to check for possible bonds?
> 
> Thank you for your assistance.
> 
> Valentin

Hi this is defined in the specbon.dat file in the distribution 

cheers
marc


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