[gmx-users] Erroneous bond in average pdb

Mark Abraham Mark.Abraham at anu.edu.au
Thu Mar 22 12:20:41 CET 2012

On 22/03/2012 9:10 PM, rama david wrote:
> 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 ??

See http://www.gromacs.org/Documentation/FAQs Analysis and visualization 
number 8 to understand whether you have a 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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