Dear AMBERist
In a simulated annealing protocol I have refined the structure of small
peptide (chimeric) using nonstandard force-fields in water with NMR
restraints on. After the MD the pdb coordinates extracted from the stable
RMSD region shows clashes ans few bad contacts. Now I want fix it. Is it
common to observe clashes after md simulation, if yes how I can fix it is
there are some software tools available?
thanks in advance...
Vince
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Received on Wed Jan 27 2016 - 06:00:07 PST
