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PostPosted: 2017.03.10 16:47 
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Joined: 2017.03.10 15:57
Posts: 2
Hey,

I have recently started to use Coral and I just can't set restrains right.

There are 3 pdb files - core_a.pdb and flexible_a.pdb make together one protein and core_b.pdb is another one. I am trying to set K140 from one protein (A) and K113 from another one (B) to be about 12 A apart. However it seems Coral is taking all my pdb files as one chain (see bellow). How can I set it correctly?

Code:
 Contacts conditions file name .......................... : dist.cnd
Condition #  1: Distance  12.000
   Between chain #  1, Residues from GLY   140 to GLY   140
       and chain #  1, Residues from GLY   378 to GLY   378
 Contacts conditions penalty ............................ : 33.54
 Contacts penalty weight ................................ : 10.00


dist.cnd:
Code:
dist 12.0
1 140 140 2 113 113


configuration:
Code:
NTER 8
core_a.pdb
LINK 14
flexible_a.pdb
CTER 20
core_b.pdb
CTER 10


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PostPosted: 2017.03.14 11:31 
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Joined: 2007.08.03 19:16
Posts: 335
Hi,

Internally Coral puts all the input proteins into one "superchain",
therefore the reported numbering is different from the dist.cnd.
Have you checked that the conbdition is fulfilled in the resulting model?


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PostPosted: 2017.03.17 11:53 
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Joined: 2017.03.10 15:57
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I have made 2 models with restrains and sadly no - the gap is about 40 A. However without restrains the models are much better.


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PostPosted: 2017.06.07 10:41 
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Joined: 2015.11.03 14:38
Posts: 12
Hi,

I thought I would just resuscitate this post because I have a similar issue... My setup is the following: one protein = domain A + short linker + domain B. The protein forms a dimer and we do know (from crystallographic data) that the domains A are dimerizing. I want to set CORAL with the pdbs of domains A and B and make it model the position of domain B in each case with the 8 AA linker.
So far, I am using a .con file with the information for the linker length (functional) and a P2 symmetry (ok). But the constraints file doesn't work...
The file is the following:
dist 5.0
1 41 62 2 262 238
dist 5.0
2 41 62 1 262 238

But I get this error:
- E -- Wrong format of conditions file
1 41 62 2 262 238
1 41 62 2 262 238

I want basically that the domains A are side by side in an anti-parallel way (aka amino acids 41/62 of domain A are next to amino acids 262/238 of domains A'). But I have no idea what is the chain numbers CORAL attributed to my bits... And I don't know if I can setup this constraints for the dimer interface only (aka not the protein monomer). Should I use different input pdbs? Any idea?
Many thanks!


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