<DIV>Dear gmx users</DIV> <DIV> </DIV> <DIV>I have a protein molecule with few missing residues,</DIV> <DIV>a Lys with CG, CD, CE, NZ missing atoms, and</DIV> <DIV>a Val with CG1, CG2 missing atoms.</DIV> <DIV>I noticed that pdb2gmx reads the pdb file and places the missing atoms.</DIV> <DIV>First I want to know whether gromacs places only missing atoms or it places the entire side chain? </DIV> <DIV>Second, is gromacs' repaired molecule reliable for simulation or I should do homology modelling using other softwares to repair the molecule?</DIV> <DIV>Thanks,</DIV> <DIV>Ninoo</DIV><p> 
        
        
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