- This topic has 2 replies, 2 voices, and was last updated 12 years, 3 months ago by Anonymous.
August 25, 2011 at 5:45 pm #1011Anonymous
Hello, I would like to be able to use the InterfaceStructMaker protocol which my lab obtained from the “svn”
(or some similar name – the database that developers use to share). I tried putting the .cc file in src/apps/public/ and then modifying the file src/apps.src.settings to contain InterfaceStructMaker after “public” : [
Here is the last bit of the stout before it stopped building. It looks like I need the file devel/init.hh since the .cc file has “#include
” and the error message said “src/apps/public/InterfaceStructMaker.cc:18:25: fatal error: devel/init.hh: No such file or directory” (see below)
I have some file by the name init.hh in two different directories:
Should I change the .cc file to be #include
, or copy init.hh into a new devel directory?
g++ -o build/src/release/linux/2.6/64/x86/gcc/apps/public/scenarios/FloppyTail.o -c -std=c++98 -pipe -ffor-scope -W -Wall -pedantic -Wno-long-long -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_38_0 -I/usr/local/include -I/usr/include src/apps/public/scenarios/FloppyTail.cc
In file included from src/protocols/moves/ThermodynamicMover.hh:23:0,
src/core/id/TorsionID_Range.hh: In function ‘bool core::id::operator<(const core::id::TorsionID_Range&, const core::id::TorsionID_Range&)':
src/core/id/TorsionID_Range.hh:108:44: warning: suggest parentheses around ‘&&’ within ‘||’
g++ -o build/src/release/linux/2.6/64/x86/gcc/apps/public/InterfaceStructMaker.o -c -std=c++98 -pipe -ffor-scope -W -Wall -pedantic -Wno-long-long -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_38_0 -I/usr/local/include -I/usr/include src/apps/public/InterfaceStructMaker.cc
src/apps/public/InterfaceStructMaker.cc:18:25: fatal error: devel/init.hh: No such file or directory
scons: *** [build/src/release/linux/2.6/64/x86/gcc/apps/public/InterfaceStructMaker.o] Error 1
scons: building terminated because of errors.
August 25, 2011 at 6:27 pm #5984Anonymous
The first question is, how did you get the file? That application hasn’t been released yet (and thus isn’t publicly supported). More relevantly, its author (Ben Stranges) warns that it hasn’t been released because it isn’t yet guaranteed to work. It is common for Rosetta labs to share copies from SVN with other labs, but generally only their own applications…
The file fails to compile because it hasn’t been converted from the “developer version” into a “release version”. Specifically, you’ll need to fix the line including devel/init.hh to instead include protocols/init.hh. It may or may not spit more errors after that. Why did you get only this one file, instead of getting a whole developer copy from SVN?
August 25, 2011 at 9:56 pm #5985Anonymous
I got it from my lab mate Eric, who signed up to have access. Let me know if I did anything “unlegit”, or if this upsets anyone as I’m new to all of this. I am interested in using it to minimize a ligand-receptor complex as stated in a document on preparing structures.
@section ben_stranges Ben’s reply
I’ve been using a protocol that does sc & bb minimization, full packing with -use_input_sc, then minimization of bb, rb, and sc. It’s located in: src/apps/pilot/stranges/InterfaceStructMaker.cc The idea with this is that it keeps things from moving too far from the starting structure. There’s no backbone sampling so I typically find rmsd to the xtal structure to be < 1.0. Relax actually will do explicit bb sampling thus gives a lower energy structure than my protocol but can also introduce the changes that you observed. I'm pasting my typical options file below:
-mute protocols.moves.RigidBodyMover protocols.moves.RigidBodyMover core.scoring.etable core.pack.task protocols.docking.DockingInitialPerturbation protocols.TrialMover core.io.database
- You must be logged in to reply to this topic.