Hi Wenjuan,
On Apr 7, 2015, at 5:00 AM, wjli <wenjuanli93.gmail.com> wrote:
> Dear Amber members,
>
> The step 8 of MCPB tutorial（building a standard model）says,"If there are less than 5 residues between two ligating residues, the bridging residues between them could be represented by GLY residues while the whole chain are capped by ACE and NME as well. "
>
> I dont understand what does it means.For example,each residue between ligand 454 and 458(455-457) should be represented by GLY residue,like 455 LEU->455GLY,but how to create 455GLY?
>
Here are the two examples about how to create GLY residue from the others:
# Create GLY-3 from ARG-138
createResidue GLY in CLR
addToResidue /1A1F/CLR/GLY-3 /1A1F/1/ARG-138 and bb_heavy
# Create GLY-4 from ILE-139
createResidue GLY in CLR
addToResidue /1A1F/CLR/GLY-4 /1A1F/1/ILE-139 and bb_heavy
> And I also has a ligand 398,ACE should be added before 398 or 454(I mean if each fragment should be capped by ACE and NME ,or the whole)?
>
They should be capped separately. For this instance, you should perform the modeling as follows:
397 to ACE
Keep 398
399 to NME
453 to ACE
Keep 454
455 to GLY
456 to GLY
457 to GLY
Keep 458
459 to NME
If you have more questions, please email me.
Hope that helps,
Pengfei
> I feel that I dont make things clear,so anywehre is unclear,just say it.
>
> Look forward to your reply!
> Best wishes.
> wjli
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Received on Tue Apr 07 2015 - 08:30:05 PDT
