Hi,
So I am trying to attach a the c-terminal of a protein to the n-terminal
of another. So far I got my proteins in the approximately correct
orientation in vmd and concatenated the translated coordinates of the
proteins into one pdb file. Now, I wanted to run energy minimization on
this file but when I tried to create the topology n coordinate files
through leap it gives me an error:
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
CGLU 1
CGLY 1
NMET 2
)
(no restraints)
quit: Improper number of arguments!
usage: quit
I still get a prmtop and inpcrd output but it somehow automatically adds a
TER card between the two proteins.
On Thu, Apr 14, 2016 at 2:42 PM, David Cerutti <dscerutti.gmail.com> wrote:
> 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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--
Thank You and Regards,
Aishani Chittoor Prem
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Received on Fri Apr 22 2016 - 12:00:04 PDT
