{maketoc}
!Difference between Eres, Ereduce, Enew?
~pp~I am running:
command executed: rosetta.gcc -design -resfile 1ubi_.resfile -cluster_design -cluster_size 2 -mutout no_interface.out -n_mutatpos 5 -repack_neighbors -s 1ubi_.pdb
And get :
#
********************************************************
ENERGY FOR WT STRUCTURE "1ubi_" is -94.6182
********************************************************
#
CONTRIBUTIONS TO THE ENERGY FOR THE WT STRUCUTRE:
#
---------------------------------------------------------------------------------------------------------------------------------
Eatr Erep Esol Eaa Edun Eintra Ehbnd Epair Eref Eh2o Eh2ohb Eh2osol Eres SASA_pack pdb name
---------------------------------------------------------------------------------------------------------------------------------
DG_BIND -219.2 22.1 113.0 -16.8 95.7 0.1 -5.4 -4.6 24.0 0.0 0.0 0.0 -94.62 3.620 1ubi_
-----------------------------------------------------------------------------------------------------------------------------------
#
******************************************************
CHANGES IN ENERGY FOR MUTANT STRUCTURES: MUT-WT
******************************************************
#
Eatr Erep Esol Eaa Edun Eintra Ehbnd Epair Eref Eh2o Eh2ohb Sasa_pack Eres Ereduce Enew N_MUT ROS# PDB# CH WT M NB ROS# PDB# CH WT M NB
DG_CALC -0.277 0.178 0.417 0.449 -0.316 -0.002 -0.939 -0.178 -0.630 0.000 0.000 0.306 -0.038 -0.799 -0.798 2 14 14 A T M 11 31 31 A Q T 16
DG_CALC -1.568 0.179 2.668 0.948 -0.623 0.001 -0.939 -0.220 -0.300 0.000 0.000 -0.826 0.745 0.160 -0.471 2 14 14 A T D 11 31 31 A Q T 16
DG_CALC -1.429 16.691 0.459 0.122 -1.006 -0.001 -0.939 -0.178 -0.870 0.000 0.000 -3.991 14.588 -1.909 -0.306 2 14 14 A T L 11 31 31 A Q T 16
Can you tell me what is the difference between Eres, Ereduce, Enew?
jens
~/pp~
!!Re: Difference between Eres, Ereduce, Enew?
These assignments are at the bottom of the design_from_cluster() subroutine in design_structure.cc
Lin Jiang is listed as the author.
!!Re: Difference between Eres, Ereduce, Enew?
It looks like this may be the pertinent code:
Eres = {CODE()}dgbind_resenergy(i+2) - dgbind_resenergy(1){CODE}
Ereduce = {CODE()}res_reduce=dgbind_atrenergy(i+2)+dgbind_solenergy(i+2)+dgbind_hbenergy(i+2)-(dgbind_atrenergy(1)+dgbind_solenergy(1)+dgbind_hbenergy(1));{CODE}
Enew = {CODE()}res_lin=0.74*(dgbind_atrenergy(i+2)-dgbind_atrenergy(1))+0.57*(dgbind_solenergy(i+2)-dgbind_solenergy(1))+0.9*(dgbind_hbenergy(i+2)-dgbind_hbenergy(1))+0.08*(dgbind_repenergy(i+2)-dgbind_repenergy(1));{CODE}
Hope that helps!
Xavier
!pNNMAKE and loops zone file
There is a section on Comparative Modeling ((Comparative Modeling)) that I just can't get to work. Does pNNMAKE actually accept a zone file? There is no mention in the nnmake code of zone file or "loops_all". This is an option in make_fragments.pl, however. Is there a newer version of pNNMAKE available?
David
!!Re: pNNMAKE and loops zone file
# I've put up Glenn's tutorial on loop modeling in the hopes that it might make things a little clearer: ((Loop Modeling))
# pNNMAKE does not accept a zone file, the zone file is for make_fragments.pl
# We are in the process of debugging the C++ version of pNNMAKE. I'm not sure when it will be available (but at this point, we are just trying to make sure it behaves like pNNMAKE).
Xavier
!How do you refine the native structure?
Hi-
I am trying to refine the native structure. Currently I idealize the native structure then relax it using the commands below. Unfortunately, this protocol sometimes generates structures high in energy, far from native. Does anyone know the correct protocol?
idealize:
rosetta.mpilam aa 1AD6 _ -timer -increase_cycles 1 -new_centroid_packing -idealize -fa_input -s 1AD6.pdb -vary_omega -omega_weight 0.5 -farlx -ex1 -ex2 -short_range_hb_weight 0.50 -long_range_hb_weight 1.0 -no_filters -nstruct 4 -paths /home/brunette/parallel_mbs/proteins/1ad6/paths_native.txt > 1ad6_abinit.log
relax:
rosetta.mpilam aa 1AD6 _ -timer -output_pdb_gz -increase_cycles 1 -new_centroid_packing -relax -fa_input -s aa1AD6_0001.pdb -vary_omega -omega_weight 0.5 -farlx -ex1 -ex2 -short_range_hb_weight 0.50 -long_range_hb_weight 1.0 -no_filters -termini -nstruct 100 -paths /home/brunette/parallel_mbs/proteins/1ad6/paths_native.txt > 1ad6_abinit.log
Thanks for the help, -TJ
!!Re: How do you refine the native structure?
Hi,
Disclaimer: I have not done too much with relax mode but ...
adding -farlx, -farlx -minimize -bb_only, or -minimize -bb_only may help reduce the structural distribution.
-Glenn
!Rosetta 2.1.1 troubleshooting
We are installing Rosetta2.1.1 - followed the directions on the quick start.
We are using FC6 - gcc
gcc is installed-
~pp~
compat-gcc-34.i386 3.4.6-4 core
compat-gcc-34-c++.i386 3.4.6-4 core
compat-gcc-34-g77.i386 3.4.6-4 core
compat-libgcc-296.i386 2.96-138 core
gcc.i386 4.1.1-51.fc6 updates
gcc-c++.i386 4.1.1-51.fc6 updates
gcc-gfortran.i386 4.1.1-51.fc6 updates
gcc-gnat.i386 4.1.1-51.fc6 updates
gcc-java.i386 4.1.1-51.fc6 updates
gcc-objc.i386 4.1.1-51.fc6 updates
gcc-objc++.i386 4.1.1-51.fc6 updates
[root@sinskey-14 ro
this is the error message -when
running - [root@sinskey-14 rosetta++]# make gcc
g++ -c -I. -IObjexxFCL -Itriplet -Iutility -Wall -W -pedantic
-Wno-unused-variable -pipe -ffor-scope -fno-exceptions -malign-double
-ffast-math -funroll-loops -finline-functions -finline-limit=20000 --param
inline-unit-growth=1000 --param large-function-growth=50000 -DNDEBUG -O3 -s
-std=c++98 -MMD -MT .gcc.version_rosetta.d -MF .gcc.version_rosetta.d -MP
version_rosetta.cc -o .gcc.version_rosetta.o
make: g++: Command not found
make: *** [.gcc.version_rosetta.o] Error 127
~/pp~
!!Re: Rosetta 2.1.1 troubleshooting
[root@sinskey-14 rosetta++]# which g++
/usr/bin/which: no g++ in (/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/X11R6/bin:/root/bin)
[root@sinskey-14 rosetta++]# which gcc
/usr/bin/gcc
[root@sinskey-14 rosetta++]# pwd
/opt/holding/rosetta++
[root@sinskey-14 rosetta++]# which gcc
/usr/bin/gcc
[root@sinskey-14 rosetta++]#
Do I have to put /usr/bin/gcc in my path to get the complier to work ?
!!Re: Rosetta 2.1.1 troubleshooting
Installed: gcc.i386 0:4.1.1-51.fc6
Dependency Installed: glibc-devel.i386 0:2.5-10.fc6 glibc-headers.i386 0:2.5-10.fc6 libgomp.i386 0:4.1.1-51.fc6
Complete!
[root@sinskey-14 rosetta++]# rpm -q gcc
gcc-4.1.1-51.fc6
[root@sinskey-14 rosetta++]#
[root@sinskey-14 rosetta++]# whereis gcc
gcc: /usr/bin/gcc /usr/lib/gcc /usr/libexec/gcc /usr/share/man/man1/gcc.1.gz
[root@sinskey-14 rosetta++]#
looks like a sim link issue ?
!!Re: Rosetta 2.1.1 troubleshooting
Thanks for the reply!
[root@sinskey-14 rosetta++]# which g++
/usr/bin/which: no g++ in (/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/X11R6/bin:/root/bin)
[root@sinskey-14 rosetta++]#
[root@sinskey-14 rosetta++]# yum install gcc.c++
Loading "installonlyn" plugin
Setting up Install Process
Setting up repositories
Reading repository metadata in from local files
Parsing package install arguments
Nothing to do
[root@sinskey-14 rosetta++]#
[root@sinskey-14 rosetta++]# make clean
rm -f rosetta.gcc rosetta.gccdebug rosetta.gccprofile
rm -f rosetta.gcc64 rosetta.gcc64debug rosetta.gcc64profile
rm -f rosetta.intel rosetta.inteldebug
rm -f rosetta.intel64 rosetta.intel64debug
rm -f rosetta.mac rosetta.macdebug
rm -f rosetta.gccmpi
rm -f .*.o ObjexxFCL/.*.o triplet/.*.o utility/.*.o boinc/.*.o
rm -f .*.d
rm -f tags TAGS
[root@sinskey-14 rosetta++]#
[root@sinskey-14 rosetta++]# make gcc
g++ -c -I. -IObjexxFCL -Itriplet -Iutility -Wall -W -pedantic -Wno-unused-variable -pipe -ffor-scope -fno-exceptions -malign-double -ffast-math -funroll-loops -finline-functions -finline-limit=20000 --param inline-unit-growth=1000 --param large-function-growth=50000 -DNDEBUG -O3 -s -std=c++98 -MMD -MT .gcc.version_rosetta.d -MF .gcc.version_rosetta.d -MP version_rosetta.cc -o .gcc.version_rosetta.o
make: g++: Command not found
make: *** [.gcc.version_rosetta.o] Error 127
so I'm confused .. gcc is not on the system - but I can grep for it above.
[root@sinskey-14 rosetta++]# rpm -q gcc
package gcc is not installed
[root@sinskey-14 rosetta++]#
!!!Re: Re: Rosetta 2.1.1 troubleshooting
>
> Thanks for the reply!
> [root@sinskey-14 rosetta++]# which g++
> /usr/bin/which: no g++ in (/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/X11R6/bin:/root/bin)
> [root@sinskey-14 rosetta++]#
So g++ is not installed or in the path and it looks like there is a typo below in the g++ package name. Try:
{CODE()}[root@sinskey-14 rosetta++]# yum install gcc-c++{CODE}
>
>
> [root@sinskey-14 rosetta++]# yum install gcc.c++
> Loading "installonlyn" plugin
> Setting up Install Process
> Setting up repositories
> Reading repository metadata in from local files
> Parsing package install arguments
> Nothing to do
X
!!Re: Rosetta 2.1.1 troubleshooting
It looks like the gnu c++ compiler (g++) can't be found. Try typing:
{CODE()}[root@sinskey-14 rosetta++]#which g++{CODE}
There should be a symbolic link /usr/bin/g++ pointing to the output of the above command.
If there was no output, I would suggest running the following command as root:
{CODE()}[root@sinskey-14 rosetta++]#yum install gcc-c++{CODE}
Before compiling, check the compiler install, by running -+which g+++- again.
I have compiled Rosetta successfully with g++ 4.1.2.
Be sure to run -+make clean+- before re-compiling.
Cheers,
Xavier
!Constraints on residue size
Hello Everyone,
In the User Guide: Ab Initio Structure Prediction it says that
......Additionally you often know information about the environment your protein exists or will exist in that is not yet taken into account by the energy function, such as boundaries on size and position of particular residue or atoms. Constrainst allow you to take advantage of such specialized knowledge....
Does anyone know how you go about set up constrainst on the size of particular residues? I am interested in mimicking the effect of glycosylating my Ser/Thr residues by increasing the volume of the centriods that represent they side chains.
Thank you all in advance
Aaron T. Frank
!!Re: Constraints on residue size
> Hello Everyone, > > In the User Guide: Ab Initio Structure Prediction it says that > ......Additionally you often know information about the environment your protein exists or will