[gmx-users] The promblem of force field

Dear, My receptor is membrane proteins,then I get protein-ligand complex.I want to do MD simulations in DPPC.I use the GROMOS96 53a6 force field modified in order to include Berger’s parameters for lipids .The topology for the ligand was created employing the server PRODRG 2.5 Beta. When I f

[gmx-users] running energy minimization error

Dear, I have finished the command "perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat",the I want to run energy minimization.I submit the command "grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr".The error like this Back Off!Ijust backed up mdout.mdp to

[gmx-users] the ligang topology

Dear, The topology for my ligand was created employing the server PRODRG 2.5 Beta. Now I change the charges to consistent with the GROMOS96,but I don't know the charges of -CF3 and C-Cl .Where can I find or can you tell me?Thanks! -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] GROMOS96 53a6 and PRODRG topologies

Dear: My receptor is membrane proteins,the I get protein-ligand complex.I want to do MD simulations in DPPC.Can I use the GROMOS96 53a6 force field modified in order to include Berger’s parameters for lipids?The topology for the ligand was created employing the server PRODRG 2.5 Beta.How to

[gmx-users] charmm-gui and gromacs

Dear: If I have used the charmm-gui to build the bilayer for the receptor-ligand complex,can I load the outcome to the gromacs to perform MD?Is the process complicated? How do it? Thanks! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users