From 94763f6dd92c61677ab8918c9caf9f9ffd608112 Mon Sep 17 00:00:00 2001 From: Adam Sieradzan Date: Thu, 20 Feb 2014 09:37:49 +0100 Subject: [PATCH] Drobne zmiany i dodanei parametrow dla dummy atom --- .gitignore | 1 + CMakeCache.txt | 40 ++++++++++++++++++++++++++++++++++++++++ CMakeFiles/cmake.check_cache | 1 + PARAM/bond_AM1_ext_dum.parm | 26 ++++++++++++++++++++++++++ PARAM/bond_ext_dum.parm | 25 +++++++++++++++++++++++++ 5 files changed, 93 insertions(+) create mode 100644 CMakeCache.txt create mode 100644 CMakeFiles/cmake.check_cache create mode 100644 PARAM/bond_AM1_ext_dum.parm create mode 100644 PARAM/bond_ext_dum.parm diff --git a/.gitignore b/.gitignore index 77a69e0..408ced9 100644 --- a/.gitignore +++ b/.gitignore @@ -28,3 +28,4 @@ bin/unres/MD-M/unres_Tc_procor_newparm_em64-D-symetr.exe DIL/ compinfo period_build +build_devel diff --git a/CMakeCache.txt b/CMakeCache.txt new file mode 100644 index 0000000..a5f54f8 --- /dev/null +++ b/CMakeCache.txt @@ -0,0 +1,40 @@ +# This is the CMakeCache file. +# For build in directory: /users2/adasko/unres +# It was generated by CMake: /users2/adasko/apps/cmake/bin/cmake +# You can edit this file to change values found and used by cmake. +# If you do not want to change any of the values, simply exit the editor. +# If you do want to change a value, simply edit, save, and exit the editor. +# The syntax for the file is as follows: +# KEY:TYPE=VALUE +# KEY is the name of a variable in the cache. +# TYPE is a hint to GUIs for the type of VALUE, DO NOT EDIT TYPE!. +# VALUE is the current value for the KEY. + +######################## +# EXTERNAL cache entries +######################## + + +######################## +# INTERNAL cache entries +######################## + +//This is the directory where this CMakeCache.txt was created +CMAKE_CACHEFILE_DIR:INTERNAL=/users2/adasko/unres +//Major version of cmake used to create the current loaded cache +CMAKE_CACHE_MAJOR_VERSION:INTERNAL=2 +//Minor version of cmake used to create the current loaded cache +CMAKE_CACHE_MINOR_VERSION:INTERNAL=8 +//Patch version of cmake used to create the current loaded cache +CMAKE_CACHE_PATCH_VERSION:INTERNAL=12 +//Path to CMake executable. +CMAKE_COMMAND:INTERNAL=/users2/adasko/apps/cmake/bin/cmake +//Path to cpack program executable. +CMAKE_CPACK_COMMAND:INTERNAL=/users2/adasko/apps/cmake/bin/cpack +//Path to ctest program executable. +CMAKE_CTEST_COMMAND:INTERNAL=/users2/adasko/apps/cmake/bin/ctest +//Path to cache edit program executable. +CMAKE_EDIT_COMMAND:INTERNAL=/users2/adasko/apps/cmake/bin/ccmake +//Path to CMake installation. +CMAKE_ROOT:INTERNAL=/users2/adasko/apps/cmake/share/cmake-2.8 + diff --git a/CMakeFiles/cmake.check_cache b/CMakeFiles/cmake.check_cache new file mode 100644 index 0000000..3dccd73 --- /dev/null +++ b/CMakeFiles/cmake.check_cache @@ -0,0 +1 @@ +# This file is generated by cmake for dependency checking of the CMakeCache.txt file diff --git a/PARAM/bond_AM1_ext_dum.parm b/PARAM/bond_AM1_ext_dum.parm new file mode 100644 index 0000000..cf2100e --- /dev/null +++ b/PARAM/bond_AM1_ext_dum.parm @@ -0,0 +1,26 @@ +1 3.800 1.900 41.7 0.000 43.0 14.33 2.5 ! peptide group and dummy atom +1 1.396 243.1 0.000 59.0 19.67 5.0 ! Cys +2 2.103 71.3 0.850 2.500 128.0 0.033 88.0 29.33 6.2 ! Met +1 2.997 124.6 0.000 104.0 34.67 6.8 ! Phe +2 1.645 260.7 0.857 1.908 312.6 .00010 70.0 23.33 6.2 ! Ile +2 1.782 638.3 2.360 2.086 160.4 0.409 70.0 23.33 6.3 ! Leu +1 1.488 294.4 0.000 56.0 18.67 5.8 ! Val +2 3.368 123.1 0.000 3.686 129.1 .00049 143.0 47.67 7.2 ! Trp +1 3.362 113.2 0.000 120.0 40.00 6.9 ! Tyr +1 0.778 353.0 0.000 28.0 9.33 4.6 ! Ala +0 14.0 0.00 3.8 ! Gly +1 1.480 295.8 0.000 58.0 19.33 5.6 ! Thr +1 1.311 269.6 0.000 44.0 14.67 4.8 ! Ser +3 2.125 147.9 2.125 2.424 138.9 .0333 2.776 383.8 0.000 85.0 28.33 6.1 ! Gln +1 2.008 161.4 0.000 71.0 23.67 5.7 ! Asn +3 2.093 131.2 1.943 2.425 146.5 .0263 2.784 479.3 0.784 85.0 28.33 6.1 ! Glu +1 2.030 160.2 0.000 71.0 23.67 5.6 ! Asp +1 2.739 134.5 0.000 95.0 31.67 6.2 ! His +3 2.644 48.8 1.707 3.433 34.8 .00123 4.080 899.9 1.175 114.0 38.00 6.8 ! Arg +3 2.379 99.0 1.974 2.704 157.5 0.546 3.073 164.7 0.055 86.0 28.67 6.3 ! Lys +1 1.422 605.2 0.000 71.0 23.67 5.6 ! Pro +2 2.142 71.3 0.850 2.500 128.0 0.033 135.0 45.00 6.2 ! SeMet +1 3.799 124.6 0.000 149.0 49.67 7.2 ! Dap(Bz) +1 0.743 353.00 0.000 42.0 14.00 4.7 ! Aib +1 1.210 353.00 0.000 42.0 14.00 5.6 ! Abu + diff --git a/PARAM/bond_ext_dum.parm b/PARAM/bond_ext_dum.parm new file mode 100644 index 0000000..2137b43 --- /dev/null +++ b/PARAM/bond_ext_dum.parm @@ -0,0 +1,25 @@ +3.800 1.900 500.00 43.0 14.33 5.0 ! peptide group and dummy +1.237 500.00 59.0 19.67 5.0 ! Cys +2.142 500.00 88.0 29.33 6.2 ! Met +2.299 500.00 104.0 34.67 6.8 ! Phe +1.776 500.00 70.0 23.33 6.2 ! Ile +1.939 500.00 70.0 23.33 6.3 ! Leu +1.410 500.00 56.0 18.67 5.8 ! Val +2.605 500.00 143.0 47.67 7.2 ! Trp +2.484 500.00 120.0 40.00 6.9 ! Tyr +0.743 500.00 28.0 9.33 4.6 ! Ala +0.000 500.00 14.0 0.00 3.8 ! Gly +1.393 500.00 58.0 19.33 5.6 ! Thr +1.150 500.00 44.0 14.67 4.8 ! Ser +2.240 500.00 85.0 28.33 6.1 ! Glu +1.684 500.00 71.0 23.67 5.7 ! Asn +2.254 500.00 85.0 28.33 6.1 ! Glu +1.709 500.00 71.0 23.67 5.6 ! Asp +2.113 500.00 95.0 31.67 6.2 ! His +3.020 500.00 114.0 38.00 6.8 ! Arg +2.541 500.00 86.0 28.67 6.3 ! Lys +1.345 500.00 71.0 23.67 5.6 ! Pro +2.142 500.00 135.0 45.00 6.2 ! SeMet +3.799 500.00 149.0 49.67 7.2 ! Dap(Bz) +0.743 500.00 42.0 14.00 4.7 ! Aib +1.210 500.00 42.0 14.00 5.6 ! Abu -- 1.7.9.5