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New parametrization problems

Submitted by DmitriiN on Wed, 2016-06-08 05:09
Category: 
Design

Hello all!

I started working with my non-canonical residue REL and found out that it doesn't bond to other residues.

Shall I write some other atoms in the end of mol file?

I am afraid only visualization can help here so I attach the mol file.

Also I attach the created with this mol file params file and one molecule with REL residue.

Thank you in advance,

Dmitrii

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Rosetta 3 - General

Parametrisation problems

Submitted by DmitriiN on Tue, 2016-05-31 09:37
Category: 
Design

Hello everyone!

I have a residue in my protein, that is non-canonical and that I named REL.

After all the steps from https://www.rosettacommons.org/demos/latest/public/design_with_ncaa/README with the only difference in using molfile_to_params.py instead of molfile_to_params_polymer.py, because the second doesn't work in my rosetta suite.

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Rosetta 3 - General

ssDNA (aptamer)/protein docking

Submitted by JulienO on Fri, 2016-05-27 02:25
Category: 
Docking

Hello everyone,

I would like to simulate the docking between a ssDNA (aptamer) and a protein. The problem is when I use the protein-protein docking it doesn't work because of the nucleic acid sequence.

Can anyone give me an exemple to realise this job ?

Thanks in advance for your help.

Best regards

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Rosetta 3 - General

CDR are not being recognized

Submitted by wildchipiron on Mon, 2016-05-23 15:03
Category: 
ROSIE

Hi!!

I had been suscesfully using ROSIE to generate Fab models for a while and lately the server has not able to recognize the CDRL3 and CDRH3 in my antibody sequences. I also tried a sequence that was previously used and modeled but now the server gave an error   

ERROR: CDR L3 cannot be recognized !!!  L3 pattern: C[A-Z]{1,15}(L|F|V|S)G[A-Z](G|Y)

and I dont undestand why  the CDR cant not be recognized now. The pattern of the input seqeunces looks correct. 

I would really aprreacite some help in this matter

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ROSIE - General

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