We can't tell you whether the two chains are supposed to be identical
or what the sulfate group is without knowing what the PDB is supposed
to be and how it was created. You need to decide what exactly you
want to calculate and whether this structure is suitable for that. At
any rate this is not an AMBER-specific question and better suited to
whoever is teaching you at your institution.
Leap knows what common residues look like so it can fill in missing
atoms. Missing residues are another matter entirely as filling these
in requires guessing how the protein folds, which is not a generally
solved problem. There are ab initio/homology modeling methods to fill
in missing residues but that many, if contiguous, is likely too many.
--Tom
On Sun, Jun 14, 2009 at 1:29 PM, <s_bill36.yahoo.co.uk> wrote:
> 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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Received on Mon Jul 06 2009 - 09:36:33 PDT
