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

[Rausch, Felix]

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.
tanks,
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