Hi everyone, I'm using this command to extract my protein and my ligand from the trajectory.
trjconv -f prot_md60ns.xtc -s prot_md50.tpr -fit rot+trans -pbc whole -n prot_wat.ndx -o prot_ligand_60ns.xtc < grps >& outtrj Before, I had a problem with residues of my protein showing at the other end of the box, when I display my .xtc with VMD. the "-pbc whole" fixed it. However, now I have another issue: my ligand is at the other end of the box. So please can anyone tell me what can I do to fix that and get a reasonable RMSD value? Thank you Carla
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