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• 23:29, 21 April 2025 Eew947 talk contribs created page Research:amber tips (Created page with "=Renumber xyz/pdb file= If you want to renumber xyz file, e.g. delete a molecule from the old xyz, you can manually remove the lines for these atoms. However, you cannot manually modify the pdb in the same way by deleting the ATOM and CONNECT entries. It will cause trouble running amber later on. (Well, no error msg would be printed out, but it stops right before the first step). The correct way is to convert xyz to pdb with xyzpdb command. =FEP-vdw= During the FEP, yo...")