[gmx-users] specbond detection
rajiv at kaist.ac.kr
Mon Apr 15 05:41:04 CEST 2013
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.
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