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Epi-Graft Match

Submitted by cruc12 on Thu, 2013-10-24 11:56

Hi,
I see the following errors when running epi-graft. What commands do I need to overcome these limits?
Thank you very much in advance for your help!

STOP :: MAX_PACK_NEIGHBORS exceeded
MAX_PACK_NEIGHBORS: 100
ERROR:: Exit from: pack.cc line: 5280

STOP:: MAX_HB_PER_ATM exceeded
ERROR:: Exit from: hbonds.cc line: 665

STOP:: acc MAX_HB_ATM exceeded
ERROR:: Exit from: hbonds.cc line: 623

STOP:: don MAX_HB_ATM exceeded
ERROR:: Exit from: hbonds.cc line: 635

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Rosetta++ - Applications

Regarding the Documentation of Rosetta and PyRosetta

Submitted by jai_INMAS on Tue, 2013-10-22 23:41

Dear members,

i m very new user of rosetta and pyrosetta i have idea about the algorithms of various molecular simulation programs like Gromacs autodock and other.

i want to know is there any documentation available about all the algorithms and methods used in Rosetta ? more precisely rather then hard core scientific notation i am looking for an easy and more descriptive documentation which can provide the information of various methods available in Rosetta.

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PyRosetta - General

using MonteCarlo to fold a random structure into a helical structure

Submitted by Run on Tue, 2013-10-22 05:48

I want to use MonteCarlo to fold a random structure into a helical stucture.But I have some troubles.
This is my script:from rosetta import *init()
p=pose_from_pdb("output3.pdb")
scorefxn=ScoreFunction()
scorefxn.set_weight(hbond_lr_bb,1.0)
scorefxn.set_weight(vdw,1.0)
ncycles=60000
KT=1.0
mc=MonteCarlo(p,scorefxn,KT)
movemap=MoveMap()
movemap.setbb(True)
small_mover=SmallMover(movemap,KT,5)
for i in range(1,ncycles):
small_mover.apply(p)
mc.boltzmann(p)
if(i%1000==0):
mc.recover_low(p)
mc.recover_low(p)
dump_pdb(p,"mc_output1.pdb")
But it told me:

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PyRosetta - Scripts

loop modeling error 'CcdLoopClosureMover' object is not callable

Submitted by jai_INMAS on Tue, 2013-10-22 01:49

I am using the current release "PyRosetta v2.012" it stucked, error is given bellow
the "loops.py" script which i m using have been attached with this post this script is provided online its not my own script: thanks

from where i can get the reference for all the available methods and function of Pyrosetta so that i can use that as per my requirement and it seems that scripts are written for different versions may not work for all the versions so how can i get the version specific details of various pyrosetta functions

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PyRosetta - General

loop modeling error 'CcdLoopClosureMover' object is not callable

Submitted by jai_INMAS on Tue, 2013-10-22 01:23

m using the current release "PyRosetta v2.012" it stucked, error is given bellow
the "loops.py" script which i m using have been attached with this post this script is provided online its not my own script: thanks

Error Log++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++Error Log
core.chemical.ResidueTypeSet: Finished initializing centroid residue type set.
Created 1980 residue types
set up job distributor
randomizing loop
low res loop modeling
Traceback (most recent call last):
File "loops.py", line 89, in
ccd(p)

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PyRosetta - Scripts

Error in loop modeling protocol its showing error "NameError: name 'ccd_closure' is not defined"

Submitted by jai_INMAS on Sun, 2013-10-20 05:22

I stuck again loop modeling protocol test file is not running. its showing error "NameError: name 'ccd_closure' is not defined"

Log+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++log

setting up movers
core.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments fr
om file test_in.frag3
core.chemical.ResidueTypeSet: Finished initializing centroid residue type set.
Created 1980 residue types
set up job distributor
randomizing loop
low res loop modeling
Traceback (most recent call last):

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PyRosetta - General

Error in loop modeling protocol

Submitted by jai_INMAS on Fri, 2013-10-18 07:08

I m trying to run the the given script loops.py its showing error

Traceback (most recent call last):
File "loops.py", line 35, in
ccd = CcdLoopClosureMover(my_loop, movemap)
NameError: name 'CcdLoopClosureMover' is not defined

Here is full log

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

C:\Users\Zebrafish\Desktop\LOOPmodeing\loop_modeling\loop_modeling>python loops.
py

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PyRosetta - General

rosetta compile with mpi options

Submitted by aa20 on Wed, 2013-10-16 21:44

Hello

I am trying to compile rosetta with mpi options on our linux based university cluster but the compilation fails with the following error,

Before compiling, I copied the site.settings.tacc.lonestar.intel into site.settings in /tools/build/, since in one of the posts it was mentioned that this is suitable for compiling on intel based clusters.

$ ./scons.py bin mode=release extras=mpi
scons: Reading SConscript files ...
Running versioning script ... fatal: Not a git repository (or any of the parent directories): .git

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Rosetta 3 - Build/Install

pmut_scan does not produce log file

Submitted by fglaser on Wed, 2013-10-16 07:25

Hi all,

I am trying to get ddG estimates for mutations on a interface. I run successfully pmut application with several different parameters, but contrary to what I understand should happen no log file is produced with the ddG info. The mutated pdb file is indeed produced with a lot of information after the coordinates are written.

But I cannot find the ddG info there....

Should a log file be produced then?

Everything seems to run fine, but as I said I cannot find the ddG info.

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Rosetta 3 - Applications

profit program in antibody design

Submitted by tzhou on Tue, 2013-10-15 23:29

I am running /tools/antibody/sample_data/command to test the functions of rosetta antibody building. Everything seems fine until

Running ProFit...
profit < grafting/details/profit-H.in > grafting/details/profit-H.out sh: profit: command not found

My question is where can I get this "profit" command?

Thank you and best wishes,
Ting

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Rosetta 3 - Applications

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