Hi everyone,
While using the PDB reader of charmm-gui for my membrane protein system which is a dimer, I got stuck at PDB manipulation option. It gives me option regarding Model missing residues where I can see:
PROA 2-4 This is N-terminal missing residues
PROB 2-4 This is N-terminal missing residues
What does it mean by Model missing residues and is it necessary to model missing residues? Shall I check both these options for model missing residues?
Also, it gives me the option for Preserve hydrogen coordinates:
Is it necessary for preserving hydrogen coordinates?
Extremely sorry, if this questions are very basic ?
With regards
You need to add the missing residues using modeller or VMD and do perform short minimization and then use this structure as a starting model for building your membrane systems.
CHARMM does add missing hydrogens at regular positions. It is not compulsory to preserve hydrogen unless your system do have specific hydrogens like protonation states etc.
I hope this helps
Follow the attached link:
https://www.researchgate.net/post/Add_missing_residues
Charmm-gui does everything without any difficulty. Read each sections
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