Re: [gmx-users] mdp file problem

madhumita das wrote: Thanks Justin, I must inform you that my pdb file has a modified cysteine residue having a mercury atom attached to the sulphur atom next to the residue having the atom 2700. Is the murcury atom creating any problem? I want Probably. Parameterizing such a species pro

Re: [gmx-users] mdp file problem

Thanks Justin, I must inform you that my pdb file has a modified cysteine residue having a mercury atom attached to the sulphur atom next to the residue having the atom 2700. Is the murcury atom creating any problem? I want to also know can I use amber forcefield in GROMACS for pdb files of lipid?

Re: [gmx-users] mdp file problem

madhumita das wrote: Hi GROMACS users, i am in the midst of simulating a protein in water. I have modified a residue in my pdb file at position 182, using amber and then acpype.py. But after running the energy minimization step,using em.mdp file generated from acpype , foll