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

[Mark Abraham]

On 4/27/2011 4:55 PM, ana johari wrote:
> 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,

See http://www.gromacs.org/Documentation/FAQs #9 and #11.

Mark



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