Can i use Modeller for fixing side chain residue in PDB file?

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Raju Dash

In my opinion, you can perform energy minimization or MD simulation to fix side chain, in case of missing residues you may select modeller to model your protein.

Ladan Mafakher

my PDB file is a complex of two protein that interact with each other. in addition my PDB file is result of MD and energy minimization. I could not model my protein by molleder because it result of interaction of two proteins . i saw that modeller can fix side chain by this command ./fix.py in.pdb> out.pdb

but i faced an error. i want to know how can use modeller to fix side chain in protein complex

Serdar Durdagi

you may also use Prime for this problem..

what is prime?

Is it a software or server?

As said Serdar Durdagi sir, you can use prime, a module of Schrodinger software. In case of moddeller, if you want to model one of the two proteins, just keep that one (may be in one chain) in your template pdb file and can do modeller.