[gmx-users] Strange output with Genbox

Jens Pohl Pohl.Jens at web.de
Wed Feb 13 14:23:22 CET 2008


I try to simulate a modified protein in a water-box. When I use genbox and have a look on the output-file then the water molecules are located in between the AA-sequence which results in an "exploding" molecule during the mdrun. I've done it several times from the very beginning, always getting a similar result (distribution of water in the AA sequence varied a bit). 

Input-sequence (AA):

Output after genbox:

Commands used (copied from .bash_history):
pdb2gmx -f 165_in.pdb -p 165 -o 165 -n 165 -i 165 -q 165_out.pdb

(used ffG53a6)

editconf -f 165 -o CbzE_ec.pdb -bt cubic -vol -d 1.0 

genbox -cp 165_ec.pdb -cs ../Water.gro -o 165_gb.pdb -p 165_gb

Thank you very much in advance for your suggestions to solve the problem

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