Are you joining terminal residue types? If so, shouldn't they be
converted (in the pdb file) to internal residue types?
Also I think the 'Marking' msg is just a warning.
Bill
On 4/22/16 11:56 AM, Aishani Prem wrote:
> 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
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
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>>
>
>
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Received on Fri Apr 22 2016 - 12:30:03 PDT
