[gmx-users] Fw: trjconv -pbc and broken reside

ana johari ana_j0000 at yahoo.com
Wed Apr 27 08:55:50 CEST 2011

dear justin,
Hello,after 5ns MD,based on your recommend, I use" 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.
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