[gmx-users] multiple peptides in the same box

[maggin]

Hi, Justin 

Thank you very much!

If I want 6 peptides in a same box, I revised it as follow:

1.pdb2gmx -f 1IYT.pdb -o 1IYT.gro -ignh -ter -water  spce  -p 1IYT.top 

2.genconf -f 1IYT.gro -nbox 1 1 1  -o 1IYTlarge_box.gro -renumber -rot
-maxrot 180 180 180

3.editconf -f 1IYTlarge_box.gro -o 1IYT_newbox.gro -c -d 1 -bt cubic 

4.genbox -cp 1IYT_newbox.gro -nmol 5  -ci 1IYT.gro -p 1IYT.top  -o
1IYT_6.gro -try 500

However, when I use VMD to check the 1IYT_6.gro, and get 12 fragments(12
proteins), actually I should get 6 fragments. 
<http://gromacs.5086.x6.nabble.com/file/n5015805/A_4SO89OF207_N%29J7%60P%5DD3J.jpg> 

<http://gromacs.5086.x6.nabble.com/file/n5015805/_AQUOZ%6042UMR8%60%24L9%7BFKDD8.jpg> 

How I fix it? Thank you very much!




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