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

Rausch, Felix frausch at ipb-halle.de
Wed Apr 27 10:19:50 CEST 2011

You could try
trjconv -f -s -pbc res -ur compact -center -o
Good luck.


Von: gmx-users-bounces at gromacs.org im Auftrag von ana johari
Gesendet: Mi 27.04.2011 08:55
An: gmx-users at gromacs.org
Betreff: [gmx-users] Fw: trjconv -pbc and broken reside

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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