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,
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
>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
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