The problem hasn't been solved
hi all,
I want to create a peptide with N-term N atom unprotonated and C-term C atom protonated.
like NH2-ALA-GLY-PRO-COOH
How to do that?
Thanks.
Hi all,
I did ab initio modeling with rosetta and then performed clustering. Initially I generated 500 decoys and then I did 1000 with a difference sequence. When I performed clustering, I still get 4 clusters yet I have not specified the number of clusters in my flags file.My question is whether this is a correct output?
Hi there,
I am trying to dock DNA to a protein (2 chains; it's a dimer), and to the best of my knowledge, there's not an out-of-the-box application that does this (there is another thread on here about that). However, I have used the RosettaScripts RosettaDNA design demo successfully, which reads, designs and scores a Protein-DNA interface.
Hi Dears,
I preformed using fragment-based loop modelling to model and get a 8 residue helix on the loop.
I generated 1000 models, now I want to filler my models to get a model with a helix on the loop,
Would you please let me know, how to find my mentioned model (i.e.,including a helix in loop area) among 1000 models.
Thanks in advance,
Ramin
Hi all,
I am trying to recreate the protocol_capture demo of RosettaScripts/RosettaDNA, but am having some difficulties reading my pdb.
I outputted by starting pdb via PyMol, and on visual inspection of the file everything looks normal. However, when I replace the sample pdb in the RosettaScripts/RosettaDNA directory, I get the output:
```
protocols.dna.util:
Finding basepairs:
There are 0 dna positions:
protocols.dna.util:
Finding basepairs:
There are 0 dna positions:
```
I am trying to prepare a structure for Rosetta and trying various flags and methods to relax the structure. One way is to use the "relax_w_allatom_cst" protocol as documented here:
https://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/d9/...
My inputs are...
Case 1. Normal relax
> /Applications/rosetta3.4/rosetta_source/bin/relax.linuxgccrelease -database /Applications/rosetta3.4/rosetta_database/ -ex1 -ex2 -relax:sequence -nstruct 1 -s mypdb.pdb
Case 2. Relax with Constraints
Hi,
I used attached "design2.xml" to design interface of Ag-Fab complex (see my previous thread). A "ddG" filter was used in the design script to calculate ddG of mutant.
After the required mutants were dumped out into PDBs, I used another very simple script (attached "ddg.xml") with just only one "ddG" filter to calculate ddG for each output PDB. When I was checking the log file, I found the ddG values calculated by two scripts are different.
For example, for the structure decoy des5xxxx_0005,
its ddG reported in log file of "design2.xml" is about -27:
I am working on using the application pepspec to identify possible peptides that would bind to a protein of interest but am running into significant difficulties at the actual peptide generation stage.
After running anchordock with three other homologous proteins in order to generate a good estimate of the anchoring residue, I
Greetings, everyone. I got the pdb file of an enzyme, but I don't know how to write the constraints of its active sites.
Could anyone help me solve this problem?
Much appreciate it.
When I open the pdb file with txteditor, I can see coordinates as:
ATOM 1 N HIS A 27 10.218 -30.379 -16.292 1.00 12.31 N
ATOM 2 CA HIS A 27 10.486 -29.045 -15.829 1.00 12.44 C
ATOM 3 C HIS A 27 11.803 -28.537 -16.417 1.00 12.46 C
ATOM 4 O HIS A 27 11.912 -27.351 -16.894 1.00 11.54 O
