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When posting build/install question please specify the following information about your system and PyRosetta version, this will allow us to answer your questions more accurate and faster:

- OS type,
- OS version
- OS arch (32 or 64bit)
for example: Ubuntu Linux 10.04 32Bit or Mac OS X 10.6

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- Python arch (32 or 64bit) if different from OS

- Version of PyRosetta including SVN revision number.

Thank you!

Post Situation: 

ligand dock into HEM containg pdb

Category: 
Docking

 Hi all

 I would like to dock  unknown chemical into PDB which have HEM as a cofactor

 But I want to fix the HEM molecule fixed during docking with constraint statement below

                 <RESIDUE_SELECTORS>
                        <ResidueName name="HEM" residue_names="HEM" residue_name3="HEM" />
                </RESIDUE_SELECTORS>
.

.

.

Post Situation: 

Scripts accompanying Hossenzadeh et al, 2001

Category: 
Design

Hi all,

I recently came across the paper titled "Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites" and wanted to try it out for myself. I downloaded the supplemental materials and tried to follow along the READMEs to test out Methods 1-4. But I am not able to actually get any of them to work even with the provided pdbs. Is anybody else having the same problem?

Here is what I have tried...

Post Situation: 

charge grid in rosetta ligand docking using rosetta script

Category: 
Docking

 

 Ho all

 Recently I'm trying to do protein-ligand docking with rosetta scripting interface

 what I want to do is to incorporate charge grid in rosetta script xml file as shown below

                 <SCORINGGRIDS ligand_chain="X" width="25" name="charge">
                        <ChargeGrid grid_name="charge" weight="1.0"/>
                </SCORINGGRIDS>
.

.

.

Post Situation: 

Questions of Cartesian_ddG calculation in PyRosetta

Category: 
PyRosetta

Dear All,

I am new to PyRosetta and I am trying to calculate the ddG after point-mutation. The calculation logic is like the following:

1) clean the pdb file and use cartesian relax to minimize its energy

2) perform the point mutation with mutate_residue() function

3) calculate the score before and after the mutation to gain the ddG

However, the ddG data I got was always positive values and have large differences from the benchmark.

Post Situation: 

Design strategy - One chain at a time OR two chains together?

Category: 
Design

Hello folks,

this is a conceptual question.

The protein I am working with has 2 domains (2 chains), and I would like to redesign part of the surface of each domain AND the interface between those domains.

I see two possibilities here (maybe there are more):

Option #1- Break the design into three smaller problems - i.e., design only chain A, then design only chain B, and finally, design the interface (5 residues + 7 residues  + 11 residues).

Post Situation: 

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