[gmx-users] specbond detection

[라지브간디]

Dear gmx,


I have mentioned the minimum distance FE bonds to C, O and NE2 (from HIS) in specbond file. As per specbond, the pdb2gmx detect these all bonds and shown in topology file. However, except the FE-C and FE-NE2, i couldn't able to visualize the bonds of FE-O and the bonds between the FE to their pyrrole nitrogen. I looked over the ffbonded.itp file and it looks fine with proper bond angle  dihdedral details. What i am missing here? 


Advance thanks for your comments.


Raju