Radius array is <= 0 for the residue: LEU ,atom: OC1
i also face similar problems ：
SER OC1,OC2 not recognized
SER 1HC1,1HC2,2HC1,2HC2 not recognized
LYS OC1,OC2 not recognized
LYS 1HC1,1HC2,2HC1,2HC2 not recognized
could you tell me what should i do?
Those OC1 atoms no not exist!
Use a proper PDB like nomenclature
And delete the hydrogens
Where is your structure coming from?
sir, both of them were acquired from gromacs.
Sir, Could i use notepad change them to O & H
Use proper PDB naming of atoms
Sir, How could i do to get the porper PDB naming of atoms
Sir, when i find like some notes “HC” , could i delete them?
and i didn’t find the changes of OC1&OC2 they should make from Internet，could you give me some advice？
You could try refining first your complex via the Haddock server refinement interface
thank you sir！！！！！！
sir,could you tell me which server i can choose to refine my complex?
sir,i choose the “energy minimization refinement”，and do not change its option.（Is this correct?）
i get a new pdb, but H,L chains are merged into one sequence. what could i do to divide them into 2 sequences？ I try to use TOOLS, but failed, I don’t know the exact steps to complete it.