Drobne zmiany i dodanei parametrow dla dummy atom

diff --git a/.gitignore b/.gitignore
index 77a69e0..408ced9 100644 (file)
--- 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 (file)
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
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+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 (file)
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 (file)
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 (file)
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