[gmx-users] Erroneous bond in average pdb

rama david ramadavidgroup at gmail.com
Thu Mar 22 11:10:33 CET 2012

Hi Gromacs Specialist,
I want to study protein aggregation study.
1. after giving the command g_anaeig -v .. -s .. -f .. -first 1 -last
1  -nframe 100 -extr ev1.pdb
    I got the pdb structure having 100 frame , but the structure have
erroneous  bonds,
    I try both VMD and pymol, but but get the same ,
What to do to solve problem ??
Should I have to do energy minimisation(IS it good idea???) ???

2. My RMSD is fluctuating in the range of 0.7 nm
    As it is generally consider good to have RMSD less than  0.4 nm in MD
    Is it the ok to study protein aggregation study or any wrong happened??
Thank you in Advance..

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