[gmx-users] connecting two chains
somayeh.alimohamadi at gmail.com
Sun Nov 2 11:02:44 CET 2014
Dear gmx users
I am performing a simulation protein- ligand by gromacs.
this protein contain two chains (A & B) which separated from eachother.
I did the following steps for pdb file
1- pdb2gmx –ignh –f initial.pdb –o initial.pdb –p topol.top -ter
2- editconf -bt cubic –f initial.pdb –o initial.pdb -c –d 0.9
3- genbox –cp initial.pdb –cs spc216.gro –o initial-box.pdb –p
4- grompp –f em.mdp –c initialbox.pdb –p topol.top –o xion.tpr
5- genion -s xion.tpr -o initial_ions.gro -p topol.top -pname NA
-nname CL -nn (number of charge)
everything was perfect, but the final pdb file has a problem which
two chains are connected eachother.
I would like to know how to solve these problems?
Ph.D Student of Medical Nanotechnology
Shahid Beheshti University of Medical Sciences
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