[gmx-users] Sucess

Tanos tccf at epq.ime.eb.br
Thu Sep 18 14:02:01 CEST 2003

    For sure Raj Badhan,
    It's quite easy to perform this.
    First you need to run make_ndx on your .tpr file like this:
                 make_ndx -f file.tpr
    This will generate your index.ndx file
    Then you should run trjconv like this:
                  trjconv -n index.ndx "filename".trr -s "filename".tpr 
-o "newfile".gro -b "time of the last frame of your dynamics" -e " time 
of the last frame of your dynamics"
    GROMACS will show a list of all groups in your system and ask you 
wich one you want to extract; Choose your protein and press enter;
    This way you are selecting only the last frame of your dynamics. 
GROMACS will generate a .gro file with the coordinates of your last 
frame that I called here "newfile.gro"
    If you want to extract your protein and your substract or drug 
together, you will have to create a new group in the menu presented when 
running make_ndx. The procedure is the following:
    1 - When running make_ndx chose h in the menu showed; GROMACS will 
show a list with the numbers of all groups in the sistem;
    2 - Verifie the numbers correponding to your protein and your 
substrate or drug;
    3 - After the character ">" type the numbers like this:  "1 | 3 | 5" 
and press enter. A new group inclunding the groups you chose will, then, 
be created;
    4 - Type "q" and press "enter"

    That's all. I hope it will be usefull for you.
    Tanos C. C. Franca.
    IME - Rio de Janeiro -  Brazil

>Dear Tanos,
>You posted a message in the Gromacs user groups about 
>extracting your protein from the water box.
>Could you let me know how you have done this as I am having 
>similar problems
>Many thanks
>Raj Badhan

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