Hi all, My protein contain some missing residues , so I rebuilt missing residues, although gap is there between helices, my idea is when do minimisation these gap should disappear. Later trying to use pdb2gmx with OPLS/aa-L FF for generating gro file for two systems containing protonated and another one is unprotonated. For protonation i used command in this way . while unprotonation didn't mention those aminoacid residues. pdb2gmx -f protin.pdb -his -asp -glu -o prot_H.gro -p pro_H.top -i pro_H.itp , grompp -f .mdp -c .gro -p .top -o out.tpr mdrun -v -deffnm out For both systems EM running fine, but when I opened in VMD, unprotonation protein helices came close means no gap. But in case of protonation it doesn't happened still gap is there between helices actually it shouldn't appear after minimisation. I tried another FF - ff43a1 result gap is disappearing for both systems. If use OPLS any options we have to mention or if we want to use OPLS -ff how to protonate the residues Any comments will be appreciated Thanks in advance
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