> You MUST (!!!) insert a TER record between the residues listed above and
> consider to introduce caps (ACE and NME) at the dangling N- and
> C-terminals". So, I have added TER statement in the PDB file between VAL
> 162 and PHE 163 residues now I can able to generate prmtop and inpcrd
> files. can you please tell me why it is asking to add TER statement and
> what it is doing???
Have you looked at the PDB with molecular graphics? (VMD, Chimera, Pymol,
...). Is there is gap where this notification is occurring? Have you
explicitly read the PDB file (i.e. are there missing residues (evidence
of disorder in the experimental structures) that are discussed in the PDB
header?)
It is not uncommon with experimental structures to have disordered regions
in the structure that cannot be defined. This leads to gaps. AMBER
cannot fill those gaps. The error message says add artificial terminii,
however this may or may not be correct based on the context. As
mentioned, reading the text based PDB file will often provide information
on missing residues, if this is an issue in this case.
If there are missing residues, you can try homology or other methods to
add back the residues (Modeller), you can add in by hand (advanced topic),
or put in the artificial gap in (via ACE/NME termini leading to a gap in
the chain which is likely not what is desired).
--tec3
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Received on Fri Mar 11 2016 - 22:30:05 PST
