For anyone interested I was able to compile on windows easily :

add #include in vertex.cpp and CNTCell.cpp

change line 29 in Job.cpp by

else if (Exe.size()>3 && (Exe.at(Exe.size()-4)!='/' && Exe.at(Exe.size()-4)!='\' ))

windows use "" so when executing it looks like ......\DTS -in input_2.dts -top top.top

cd dts_src
cl /O2 /EHsc *.cpp
cl /FeDTS *.obj
move DTS.exe ...

cd ..
cd dts_convert
cl /O2 /EHsc *.cpp
cl /FeCNV *.obj
move CNV.exe ...

cd ..
cd dts_generate
cl /O2 /EHsc *.cpp
cl /FeGEN *.obj
move GEN ...
cd ..

Hi, my aim is to place the curvature protein on the two side of the membrane, does it possible to use FreeDTS to do that ?and how can i change the inclusion parameter to do that?

Thank you very much