We have experimental data for two ligands, we are trying to fit this data with Autodock vina results so we can increase the weightage of Hydrogen bond and Hydrophobic interactions.
Here our main goal is getting energy value for already defined pose so we want to get all the conformations with energy value which we mentioned in number of modes.
eg:-
If number of mode =50 mean we want to get these all 50 conformation with energy value.
NOTE: Even I tried the option changing energy_range but I couldn't get all conformations, could someone help me to resolve this problem?
Thanks for your kind reply,
yes, I tried with 50 modes also but I got only 20 conformations as a output.
I remember I've changed the source code for this reason :) I can give the diff if you like.
Thank you for your kind reply
Sure , If It is works I will be really Tthankful for you
Change in main.cpp
par.mc.num_saved_mins = 20;
to
par.mc.num_saved_mins = num_modes;
This one:
http://vina.scripps.edu/download/autodock_vina_1_1_2/src/main/main.cpp
Dear Sergei ,
whatevr you told is correct when we have souce file but we are having only vina and vina_split binary files with software package so in such cases how can i do this ?
Download the source, modify and compile. Should be straightforward.
Dear Sergei,
I tried to install vina sorce file on my system but I am getting error like this
"
../../../src/lib/quaternion.h: In function ‘void quaternion_normalize(qt&)’:
../../../src/lib/quaternion.h:79: error: ‘quaternion_is_normalized’ was not declared in this scope
../../../src/lib/quaternion.h: In function ‘void quaternion_normalize_approx(qt&, fl)’:
../../../src/lib/quaternion.h:91: error: ‘quaternion_is_normalized’ was not declared in this scope
make: *** [main.o] Error 1 "
could you help me to solve this error.
Thank you
Dear Sergei,
I get an error during the build:
/usr/bin/ld: cannot find -lboost_system1_41_0
/usr/bin/ld: cannot find -lboost_thread1_41_0
/usr/bin/ld: cannot find -lboost_serialization1_41_0
/usr/bin/ld: cannot find -lboost_filesystem1_41_0
/usr/bin/ld: cannot find -lboost_program_options1_41_0
collect2: ld returned 1 exit status
make: *** [vina] Error 1
could you help me to solve this error
Thank you
Dear all,
If someone getting above two errors, please follow this steps.
Solution for first Error:
We should not compile Make file which is present in Debug folder
Incase If you execute you will get error like this
"
../../../src/lib/quaternion.h: In function ‘void quaternion_normalize(qt&)’:
../../../src/lib/quaternion.h:79: error: ‘quaternion_is_normalized’ was not declared in this scope
../../../src/lib/quaternion.h: In function ‘void quaternion_normalize_approx(qt&, fl)’:
../../../src/lib/quaternion.h:91: error: ‘quaternion_is_normalized’ was not declared in this scope
make: *** [main.o] Error 1 "
Solution for second Error:
This error because of inproper Make file.
I have given correct format of make file.
-----------------------------------------------------------------------------
BASE=/usr/local
BOOST_VERSION=1_41_0
BOOST_INCLUDE = $(BASE)/include
C_PLATFORM=-static -pthread
GPP=/usr/bin/g++
C_OPTIONS= -O3 -DNDEBUG
BOOST_LIB_VERSION=
include ../../makefile_common
--------------------------------------------------------------------------------
/usr/bin/ld: cannot find -lboost_system1_41_0
/usr/bin/ld: cannot find -lboost_thread1_41_0
/usr/bin/ld: cannot find -lboost_serialization1_41_0
/usr/bin/ld: cannot find -lboost_filesystem1_41_0
/usr/bin/ld: cannot find -lboost_program_options1_41_0
collect2: ld returned 1 exit status
make: *** [vina] Error 1
Dear Sergei,
I have edited main.cpp like as you mentioned in the previous replys and its works fine .
Thank you somuch for your kind help dear friend :-)
Does anyone have a copy of the compiled executables? I am having problems compiling as well.
Dear Brian,
What do you mean by compiled executables? Do you want compiled main.cpp file or vina_source file ? Anyway i have attached zip file along with this message which has all the sources for vina to provide multiple conformations.
Thanks to your generosity I have saved some time in compiling vina for more confs
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