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 topol.top 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? regards -- Somayeh Alimohammadi Ph.D Student of Medical Nanotechnology Shahid Beheshti University of Medical Sciences Tehran-Iran -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.