minor fix: remove "./top/" directory from the topology file.

bondrewd · Feb 16, 2022 · 0de6968 · 0de6968
1 parent d1c4b26
commit 0de6968
Show file tree

Hide file tree

Showing 16 changed files with 728 additions and 1,037 deletions.
diff --git a/src/lib/parser_top.jl b/src/lib/parser_top.jl
@@ -44,7 +44,7 @@ function write_grotop(top::GenTopology, system_name::AbstractString, args::Dict{
     print(top_file, "\n")
 
     print(top_file, "; Molecule topology \n")
-    print(top_file, "#include \"./top/", itp_name, "\" \n\n")
+    print(top_file, "#include \"", itp_name, "\" \n\n")
 
     print(top_file, "[ system ] \n")
     print(top_file, system_name, " \n\n")

diff --git a/test/coarse-graining/DNA_cg_ref.cif b/test/coarse-graining/DNA_cg_ref.cif
diff --git a/test/coarse-graining/DNA_cg_ref.gro b/test/coarse-graining/DNA_cg_ref.gro
@@ -1,4 +1,4 @@
-CG model DNA_x3dna_new_cg, t =            0.000 
+CG model DNA_test_cg, t =            0.000 
          178 
     1   DA   DS    1  -0.2790   0.6611  -0.0769   0.0000   0.0000   0.0000 
     1   DA   DB    2  -0.0440   0.2425   0.0012   0.0000   0.0000   0.0000 
@@ -178,5 +178,5 @@ CG model DNA_x3dna_new_cg, t =            0.000
    60   DT   DP  176  -0.0345  -0.9265   0.1840   0.0000   0.0000   0.0000 
    60   DT   DS  177  -0.2848  -0.6597   0.0978   0.0000   0.0000   0.0000 
    60   DT   DB  178  -0.0036  -0.3380   0.0020   0.0000   0.0000   0.0000 
-         0.0000         0.0000         0.0000 
+         2.2157         2.5310         9.7627 
 
diff --git a/test/coarse-graining/DNA_cg_ref.itp b/test/coarse-graining/DNA_cg_ref.itp
diff --git a/test/coarse-graining/DNA_cg_ref.pdb b/test/coarse-graining/DNA_cg_ref.pdb
diff --git a/test/coarse-graining/DNA_cg_ref.psf b/test/coarse-graining/DNA_cg_ref.psf
diff --git a/test/coarse-graining/DNA_cg_ref.top b/test/coarse-graining/DNA_cg_ref.top
@@ -0,0 +1,38 @@
+; common interaction parameters for CG models
+#include "./param/atom_types.itp" 
+; AICG2+ flexible local angle parameters 
+#include "./param/flexible_local_angle.itp" 
+; AICG2+ flexible local dihedral parameters 
+#include "./param/flexible_local_dihedral.itp" 
+; residue-residue potential parameters (Miyazawa-Jernigan-1996-JMB) 
+#include "./param/pair_energy_MJ_96.itp" 
+
+; Molecule topology 
+#include "DNA_test_cg.itp" 
+
+[ system ] 
+DNA_test_cg 
+
+[ molecules ] 
+DNA_test_cg  1 
+
+; [ cg_ele_chain_pairs ] 
+; ON 1 - 2 : 3 - 4 
+; OFF 1 - 1 : 3 - 3 
+; OFF 1 - 1 
+
+; [ pwmcos_chain_pairs ] 
+; ON 1 - 2 : 3 - 4 
+; OFF 1 - 1 : 3 - 3 
+; OFF 2 - 3 
+
+; [ pwmcosns_chain_pairs ] 
+; ON 1 - 2 : 3 - 4 
+; OFF 1 - 1 : 3 - 3 
+; OFF 2 - 3 
+
+; [ cg_KH_chain_pairs ] 
+; A 1 - 2 : 3 - 4 
+; OFF 1 - 1 : 3 - 3 
+; OFF 2 - 3 
+
diff --git a/test/coarse-graining/FUS_cg_ref.gro b/test/coarse-graining/FUS_cg_ref.gro
@@ -163,5 +163,5 @@ CG model FUS_cg, t =            0.000
   161  TYR   CA  161   0.0000   0.0000  60.8000   0.0000   0.0000   0.0000 
   162  ASN   CA  162   0.0000   0.0000  61.1800   0.0000   0.0000   0.0000 
   163  SER   CA  163   0.0000   0.0000  61.5600   0.0000   0.0000   0.0000 
-         0.0000         0.0000         0.0000 
+         0.0000         0.0000        61.5600 
 
diff --git a/test/coarse-graining/FUS_cg_ref.top b/test/coarse-graining/FUS_cg_ref.top
@@ -8,7 +8,7 @@
 #include "./param/pair_energy_MJ_96.itp" 
 
 ; Molecule topology 
-#include "./top/FUS_cg.itp" 
+#include "FUS_cg.itp" 
 
 [ system ] 
 FUS_cg 

diff --git a/test/coarse-graining/Makefile b/test/coarse-graining/Makefile
@@ -55,16 +55,15 @@ clean_TAL:
 	rm -f TAL_cg.{log,itp,psf,pdb,gro,top}
 
 run_DNA:
-	../../tools/modeling/DNA_3SPN.2C/bdna_3spn2c_gen.sh DNA.fasta
+	../../tools/modeling/DNA_general/build_dna.jl -s DNA.fasta -C -o DNA_test
 
 diff_DNA:
-	diff DNA_x3dna_new_cg.gro DNA_cg_ref.gro || exit 0
-	diff DNA_x3dna_new_cg.pdb DNA_cg_ref.pdb || exit 0
-	diff DNA_x3dna_new_cg.psf DNA_cg_ref.psf || exit 0
-	diff DNA_x3dna_new_cg.itp DNA_cg_ref.itp || exit 0
+	diff DNA_test_cg.gro DNA_cg_ref.gro || exit 0
+	diff DNA_test_cg.cif DNA_cg_ref.cif || exit 0
+	diff DNA_test_cg.itp DNA_cg_ref.itp || exit 0
 
 clean_DNA:
-	rm -f DNA_x3dna*
+	rm -f DNA_test*
 
 run_TBP:
 	../../src/aa_2_cg.jl --pwmcos --pwmcos-scale 2.0 --pwmcos-shift -3.14159 --pfm TBP.pfm TBP.pdb

diff --git a/test/coarse-graining/ROM_cg_ref.gro b/test/coarse-graining/ROM_cg_ref.gro
@@ -115,5 +115,5 @@ CG model ROM_cg, t =            0.000
   113  PHE   CA  113   4.7130  -0.8549   0.5997   0.0000   0.0000   0.0000 
   114  GLY   CA  114   4.8435  -1.0172   0.2778   0.0000   0.0000   0.0000 
   115  ASP   CA  115   5.1484  -1.1686   0.4579   0.0000   0.0000   0.0000 
-         0.0000         0.0000         0.0000 
+         4.3345         2.2022         3.4020 
 
diff --git a/test/coarse-graining/TAL_cg_ref.gro b/test/coarse-graining/TAL_cg_ref.gro
@@ -585,5 +585,5 @@ CG model TAL_cg, t =            0.000
   521   RA   RP  583   3.7787  -0.2428   1.9456   0.0000   0.0000   0.0000 
   521   RA   RS  584   3.3939  -0.3411   1.7887   0.0000   0.0000   0.0000 
   521   RA   RB  585   3.4478  -0.9374   1.6768   0.0000   0.0000   0.0000 
-         0.0000         0.0000         0.0000 
+         6.2745         6.3242         6.7067 
 
diff --git a/test/coarse-graining/VP_cg_ref.gro b/test/coarse-graining/VP_cg_ref.gro
@@ -244,5 +244,5 @@ CG model VP_cg, t =            0.000
   242  PHE   CA  242   7.9284   1.3812  18.6730   0.0000   0.0000   0.0000 
   243  TYR   CA  243   8.2975   1.3054  18.7082   0.0000   0.0000   0.0000 
   244  ALA   CA  244   8.5278   1.0526  18.5401   0.0000   0.0000   0.0000 
-         0.0000         0.0000         0.0000 
+         4.6759         3.4225         5.5256