AMBER Archive (2009)

Subject: [AMBER] PLEASE HELP - PDB Modification

From: s_bill36_at_yahoo.co.uk
Date: Sun Jun 14 2009 - 12:29:31 CDT

Dear AMBER User's
I am a new student using AMBER. In my PDB file, I have two Chains (A and B), chain A has 51 missing residues and chain B has 35 residue missing. Is it normal? should they be identical?
In this case, it will be better for me to pick up chain B, isn't it?
Should I build this missing residues in Xleap before running my jobs? becuase I found that Xleap doesn't add the missing residues like does with missing atoms.
Last point, I found SO4 group in my PDB, not in the active site, should I delete it like extra water?
Thanks in advance

      
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