[gmx-users] pdb2gmx and his-heme group

[Mark Abraham]

Anthony Cruz Balberdi wrote:
> Hi user: 
>  
> Today I have been working with a heme protein and I notice that in the topology the parameters that include the His 
> (NE2) and the heme (FE) were not present in the topology (bon type, angle type, etc). Also when I check the topology 
> after grompp (-pp) this file also do not include the parameters. This is normal?? I am using gromacs 3.2.1 . 

Were they present as residues in the .rtf file? Did you read the 
warnings from pdb2gmx and/or grompp about things being missing?

Mark