[gmx-users] specbonds not shwon

라지브간디 rajiv at kaist.ac.kr
Fri Apr 19 08:46:26 CEST 2013

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. 



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