[gmx-users] trjconv

[ana johari]

Hello dear user,
after 5ns MD,I used trjconv  -f  -s -pbc -mol -center -o *.pdb command to get 
the whole protein without any separation,but I found some part of the residue 
was broken,and some new bond at the end of some residue was formed.I need the 
intact molecule for docking,but how should I solve this problem.
any advice was appreciate.
tanks,
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