Dear Justin,
I understand all the visualization programs guess the chemical bonds..etc. When i use ngmx i can able to see the bonds which i mentioned in topology but none of the other program such as vmd, pymol, chimera fails to shows them. Is there anyway i can make other visualization program to show off? 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? > What appears in visualization software is not definitive. The topology is. http://www.gromacs.org/Downloads/Related_Software/Visualization_Software#Topology_bonds_vs_Rendered_bonds -Justin
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