I'm sure you could do it with Amber (you can probably just concatenate the
PDB files such that there is no TER card between the two proteins, and
tleap will pick this up as a long bond between an otherwise continuous
peptide chain). However, the best practice is probably to use some other
software such as VMD to first get the two proteins into roughly the correct
orientation. Then, you can use Amber.
Proceed as I said to orient the proteins, print back the rotated /
translated coordinates to new PDB files and concatenate them. Start your
energy minimization very conservatively. Use restraints on many backbone
atoms of each protein, aside from the C-terminal residues of the one and
the N-terminal residues of the other. The basic tutorials on protein
simulation setup now start to apply. Let the minimization then pull the
termini into a decent-looking linker region: make sure to check the
chirality of all of those residues after you are done! Once that's
finished you can use ambpdb to make a new PDB file and visualize the
structure, or just read in the topology and minimized coordinates to look
at it in VMD. At that point all of the standard operating procedures
should apply.
Dave
On Thu, Apr 14, 2016 at 5:30 PM, Aishani Prem <aishaniprem.gmail.com> wrote:
> Hi,
> I am trying to attach c-terminal of a protein1 to the n-terminal of
> protein2 and then run energy minimization on it. Is it possible to do this
> using amber?
>
> --
> Thank You and Regards,
> Aishani Chittoor Prem
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>
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Received on Thu Apr 14 2016 - 15:00:04 PDT
