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enzyme design and output_matchres_only

Submitted by petrikigor on Wed, 2012-10-24 18:45

I have successfully been able to run match, but enzdes remains elusive. Currently, I'm trying to figure out, if I used output_matchres_only in matcher (my PDB files only contain the ligand and catalytic residues), how do I load both the pdb file containing the scaffold and pdb files containing the matched site into enzyme design?

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How to calculate dG?

Submitted by yperez on Mon, 2012-10-22 07:28

Hi all,
I have modeled some mutations with the Backrub application and would like to calculate dG of folding (to do somthing similar to ddG monomer application). Is there a way to do this? Thanks.

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match_dspos1 and other matcher options

Submitted by petrikigor on Sat, 2012-10-20 09:22

I am just wondering about the options for matching. Particularly, the manual says:

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AtomTree::torsion_angle() can't find dof! in match and enzdes

Submitted by petrikigor on Fri, 2012-10-19 09:49

I am running matcher and enzdes using a complex ligand. I keep getting the following lines repeating throughout my output files in both matching and enzdes:
core.kinematics.AtomTree: AtomTree::torsion_angle() cant find dof! atomno= 6 rsd= 5 atomno= 9 rsd= 5 atomno= 10 rsd= 5 atomno= 11 rsd= 5 core.kinematics.AtomTree: AtomTree::torsion_angle() cant find dof! atomno= 6 rsd= 5 atomno= 9 rsd= 5 atomno= 14 rsd= 5 atomno= 15 rsd= 5

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Unknow atom_name: LYS 1HZ in enzdes after match

Submitted by petrikigor on Fri, 2012-10-19 09:35

I am trying to run enzyme design on one of the models that I got from a matcher run, but it fails with the following:
protocols.toolbox.match_enzdes_util.EnzConstraintParameters: for block 1, 1 newly generated constraints were added protocols.toolbox.match_enzdes_util.EnzConstraintIO: checking cst data consistency for block 1... done protocols.toolbox.match_enzdes_util.EnzConstraintIO: Cst Block 1done... protocols.toolbox.match_enzdes_util.EnzConstraintParameters: for block 2, 1 newly generated constraints were added

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Error when importing protocols.simple_filters

Submitted by xfliu on Tue, 2012-10-16 13:37

Hi,

I'm trying to access ddG filter in PyRosseta. But it seems that the simple_filters module is not implemented in current PyRosetta r51661, because the following errors occurred when I trying do so:

>>> from rosetta import *
>>> import rosetta.protocols.simple_filters

Traceback (most recent call last):
File "", line 1, in
import rosetta.protocols.simple_filters
File "D:\Program Files\PyRosetta\rosetta\protocols\simple_filters\__init__.py", line 1, in
from __simple_filters_all_at_once_ import *

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PyRosetta - General

Fixbb Multiple Resfiles

Submitted by protos_heis on Mon, 2012-10-15 10:34

I was wondering if it is possible to specify multiple resfiles in a single fixbb job submission. For instance, if I have 10 resfiles and 10 PDBs I would like to have 100 output files, 10 for each resfile. If not is there a simple way to modify the code to do this? I tried writing a wrapper program for the main function in fixbb.cc that cycles resfiles in and out of the flags file and calls the main function passing that in as argv, but the second call to the main function (second resfile) crashes with an error message saying:

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AbinitioRelax usage (3.4)

Submitted by atruong on Fri, 2012-10-12 13:38

I'm trying to run AbinitioRelax on a cluster (remotely), but I keep getting the error that there is no such file or directory when the executable tries to release. My command is as follows:

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Symmetric Processing for evaluating side-chain of chi angle

Submitted by qlj on Wed, 2012-10-10 04:08

I have some problems about evaluating side-chain of chi angle. I used executable file of "relax" to repack side-chain, then I want to evaluate the number of chi angles which are lower than 40 degrees comparing with native angle. I associate something, as follows:
1、amino acids ,like ASP , GLU, PHE, TYR, ARG, etc ,having symmetry, are evaluated with symmetrical processing, in order to avoid error calculation coursed by the numbers of the same atomic.

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