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
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