[gmx-users] heme topology

Marc Ceruso mceruso at physbio.mssm.edu
Sat Jun 22 15:54:19 CEST 2002

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 


> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list