[gmx-users] specbond detection

[Justin Lemkul]

On 4/14/13 11:41 PM, 라지브간디 wrote:
> 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

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================