On Fri, Jun 28, 2019, Chetna Tyagi wrote:
>
>I work with a big protein with roughly 1000 residues. The PDB structure has
>missing residues which causes problem during equilibration.
>
>Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 0 5803 11719 11720
Running pdb4amber will identify those gaps, so you can address them, say
be inserting a TER card between non-connected residues.
But the problem of how to figure what what portion of a very
large protein can be ignored during a simulation is not one that has a
general solution. Look at the domain structure of your system, and
consider whether you could work with just a ligand-binding domain.
....dac
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Received on Sun Jun 30 2019 - 06:00:08 PDT
