diff --git a/images/ALA/data.png b/images/ALA/data.png new file mode 100644 index 00000000..7120741b Binary files /dev/null and b/images/ALA/data.png differ diff --git a/images/ARG/data.png b/images/ARG/data.png new file mode 100644 index 00000000..13620b6d Binary files /dev/null and b/images/ARG/data.png differ diff --git a/images/ASN/data.png b/images/ASN/data.png new file mode 100644 index 00000000..8835aa94 Binary files /dev/null and b/images/ASN/data.png differ diff --git a/images/ASP/data.png b/images/ASP/data.png new file mode 100644 index 00000000..03559074 Binary files /dev/null and b/images/ASP/data.png differ diff --git a/images/CYS/data.png b/images/CYS/data.png new file mode 100644 index 00000000..372cf2b3 Binary files /dev/null and b/images/CYS/data.png differ diff --git a/images/GLN/data.png b/images/GLN/data.png new file mode 100644 index 00000000..f945d9f8 Binary files /dev/null and b/images/GLN/data.png differ diff --git a/images/GLU/data.png b/images/GLU/data.png new file mode 100644 index 00000000..1d434f44 Binary files /dev/null and b/images/GLU/data.png differ diff --git a/images/GLY/data.png b/images/GLY/data.png new file mode 100644 index 00000000..6bb49c59 Binary files /dev/null and b/images/GLY/data.png differ diff --git a/images/HIS/data.png b/images/HIS/data.png new file mode 100644 index 00000000..219af9bd Binary files /dev/null and b/images/HIS/data.png differ diff --git a/images/ILE/data.png b/images/ILE/data.png new file mode 100644 index 00000000..2cd32671 Binary files /dev/null and b/images/ILE/data.png differ diff --git a/images/LEU/data.png b/images/LEU/data.png new file mode 100644 index 00000000..1f0c0d53 Binary files /dev/null and b/images/LEU/data.png differ diff --git a/images/LYS/data.png b/images/LYS/data.png new file mode 100644 index 00000000..9cf29ed5 Binary files /dev/null and b/images/LYS/data.png differ diff --git a/images/MET/data.png b/images/MET/data.png new file mode 100644 index 00000000..a9198dee Binary files /dev/null and b/images/MET/data.png differ diff --git a/images/PHE/data.png b/images/PHE/data.png new file mode 100644 index 00000000..00a92799 Binary files /dev/null and b/images/PHE/data.png differ diff --git a/images/PRO/data.png b/images/PRO/data.png new file mode 100644 index 00000000..7ab0cc33 Binary files /dev/null and b/images/PRO/data.png differ diff --git a/images/SER/data.png b/images/SER/data.png new file mode 100644 index 00000000..44292e17 Binary files /dev/null and b/images/SER/data.png differ diff --git a/images/THR/data.png b/images/THR/data.png new file mode 100644 index 00000000..3cccaa61 Binary files /dev/null and b/images/THR/data.png differ diff --git a/images/TRP/data.png b/images/TRP/data.png new file mode 100644 index 00000000..f51db961 Binary files /dev/null and b/images/TRP/data.png differ diff --git a/images/TYR/data.png b/images/TYR/data.png new file mode 100644 index 00000000..29f8f303 Binary files /dev/null and b/images/TYR/data.png differ diff --git a/images/VAL/data.png b/images/VAL/data.png new file mode 100644 index 00000000..8ead6586 Binary files /dev/null and b/images/VAL/data.png differ diff --git a/images/all_aa_sim.png b/images/all_aa_sim.png new file mode 100644 index 00000000..4cc7430c Binary files /dev/null and b/images/all_aa_sim.png differ diff --git a/images/ss_populations.png b/images/ss_populations.png new file mode 100644 index 00000000..7a0ce16d Binary files /dev/null and b/images/ss_populations.png differ diff --git a/multi-ego-basic.ff/ffbonded.itp b/multi-ego-basic.ff/ffbonded.itp index b4d4c66a..f99c2eb9 100644 --- a/multi-ego-basic.ff/ffbonded.itp +++ b/multi-ego-basic.ff/ffbonded.itp @@ -379,65 +379,64 @@ #define gd_42A 100.0000 3.0000 2 ; Backbone dihedral angle -N-CA-C-N- ALA ; -#define gd_43A 15.0000 2.800 3 ;heigher k to shift down J coupling and have a cleaner distinction between betas +#define gd_43A 25.0000 0.000 4 ;heigher k to shift down J coupling and have a cleaner distinction between betas ; Backbone dihedral angle -C-N-CA-C- ALA ; -#define gd_44A 170.000 3.0 1 +#define gd_44A 160.000 3.0 1 ; Backbone dihedral angle -C-N-CA-C- ALA ; -#define gd_45A 180.00 3.00 1 +#define gd_45A 180.00 4.00 1 ; Backbone dihedral angle -N-CA-C-N- ALA ; ;;;;;;;;;;;;;;;;;;;; ; ASN ;;;;;;;;;;;;;;;;;;;; -#define gd_42N 100.0000 1.5000 2 +#define gd_42N 100.0000 1.0000 2 ; Backbone dihedral angle -N-CA-C-N- ASN ; -#define gd_43N -35.0000 1.700 3 +#define gd_43N -80.0000 1.900 3 ; Backbone dihedral angle -C-N-CA-C- ASN ; -#define gd_44N -85.000 2.7 1 +#define gd_44N -90.000 2.0 1 ; Backbone dihedral angle -C-N-CA-C- ASN ; -#define gd_44Nb 30.000 2.2 4 +#define gd_44Nb 0.000 1.6 4 ; Backbone dihedral angle -C-N-CA-C- ASN ; -#define gd_45N 0.00 1.6 1 +#define gd_45N -90.00 1.0 1 ; Backbone dihedral angle -N-CA-C-N- ASN ; ;;;;;;;;;;;;;;;;;;;; ; ASP ;;;;;;;;;;;;;;;;;;;; -#define gd_42D 120.0000 2.5000 2 +#define gd_42D 120.0000 0.5000 2 ; Backbone dihedral angle -N-CA-C-N- ASP ; -#define gd_43D 15.0000 1.200 3 +#define gd_43D 15.0000 0.000 3 ; Backbone dihedral angle -C-N-CA-C- ASPl ; -#define gd_44D -150.000 2.60 1 +#define gd_44D -150.000 2.40 1 ; Backbone dihedral angle -C-N-CA-C- ASP ; -#define gd_45D 180.00 2.0 1 +#define gd_45D 0.00 1.5 1 ; Backbone dihedral angle -N-CA-C-N- ASP ; ;;;;;;;;;;;;;;;;;;;; ; CYS ;;;;;;;;;;;;;;;;;;;; -#define gd_42C 30.0000 2.0000 2 +#define gd_42C 100.0000 1.2000 2 ; Backbone dihedral angle -N-CA-C-N- CYS ; -#define gd_43C 70.0000 2.200 3 ; lower k for higher J coupling and more population in intermediate beta region +#define gd_43C 70.0000 0.000 3 ; lower k for higher J coupling and more population in intermediate beta region ; Backbone dihedral angle -C-N-CA-C- CYS ; -#define gd_44C 68.000 3 1 +#define gd_44C -150.000 2.5 1 ; Backbone dihedral angle -C-N-CA-C- CYS ; -#define gd_43Cb -10.0000 2.700 2 ; lower k for higher J coupling and more population in intermediate beta region +#define gd_43Cb -110.0000 1.000 2 ; lower k for higher J coupling and more population in intermediate beta region ; Backbone dihedral angle -C-N-CA-C- CYS ; -; -#define gd_45C 0.00 5.50 1 +#define gd_45C 0.00 2.50 1 ; Backbone dihedral angle -N-CA-C-N- CYS ; ;;;;;;;;;;;;;;;;;;;; @@ -446,30 +445,31 @@ #define gd_42E 90.0000 2.5000 2 ; Backbone dihedral angle -N-CA-C-N- GLU ; -#define gd_43E 15.0000 2.60 3 ;heigher k to shift down J coupling and have a cleaner distinction between betas +#define gd_43E 15.0000 0.00 3 ;heigher k to shift down J coupling and have a cleaner distinction between betas ; Backbone dihedral angle -C-N-CA-C- GLU ; #define gd_44E -160.000 1.50 1 ; Backbone dihedral angle -C-N-CA-C- GLU ; -#define gd_45E 180.00 2.900 1 +#define gd_45E 180.00 2.500 1 ; Backbone dihedral angle -N-CA-C-N- GLU ; ;;;;;;;;;;;;;;;;;;;; ; HIS ;;;;;;;;;;;;;;;;;;;; -#define gd_42H 80.0000 2.5000 2 +#define gd_42H 100.0000 1.9000 2 ; Backbone dihedral angle -N-CA-C-N- HIS ; -#define gd_43H -50.0000 2.70 3 +#define gd_43H 30.0000 0.000 3 ; Backbone dihedral angle -C-N-CA-C- HIS ; -#define gd_44H -25.000 1.60 1 +#define gd_44H -150.000 2.00 1 ; Backbone dihedral angle -C-N-CA-C- HIS -#define gd_44Hb 40.000 2.40 4 +; +#define gd_44Hb 60.000 0.50 4 ; Backbone dihedral angle -C-N-CA-C- HIS ; -#define gd_45H 0.00 3.0 1 +#define gd_45H 0.000 2.0 1 ; Backbone dihedral angle -N-CA-C-N- HIS ; ;;;;;;;;;;;;;;;;;;;; @@ -481,7 +481,7 @@ #define gd_43L 15.0000 0.600 3 ; Backbone dihedral angle -C-N-CA-C- LEU ; -#define gd_44L -160.000 2.5 1 +#define gd_44L -160.000 1.5 1 ; Backbone dihedral angle -C-N-CA-C- LEU ; #define gd_45L 180.00 2.0 1 @@ -493,13 +493,13 @@ #define gd_42M 90.0000 2.5000 2 ; Backbone dihedral angle -N-CA-C-N- MET ; -#define gd_43M 15.0000 0.600 3 +#define gd_43M 15.0000 0.000 3 ; Backbone dihedral angle -C-N-CA-C- MET ; #define gd_44M -160.000 3.0 1 ; Backbone dihedral angle -C-N-CA-C- MET ; -#define gd_45M 180.00 1.8 1 +#define gd_45M 180.00 0.6 1 ; Backbone dihedral angle -N-CA-C-N- MET ; ;;;;;;;;;;;;;;;;;;;; @@ -508,31 +508,31 @@ #define gd_42R 95.0000 2.0000 2 ; Backbone dihedral angle -N-CA-C-N- ARG ; -#define gd_43R 15.0000 1.600 3 +#define gd_43R 15.0000 0.000 3 ; Backbone dihedral angle -C-N-CA-C- ARG ; -#define gd_44R -150.000 2.50 1 +#define gd_44R -160.000 2.50 1 ; Backbone dihedral angle -C-N-CA-C- ARG ; -#define gd_45R 180.000 2.50 1 +#define gd_45R 180.000 1.50 1 ; Backbone dihedral angle -N-CA-C-N- ARG ; ;;;;;;;;;;;;;;;;;;;; ; TRP ;;;;;;;;;;;;;;;;;;;; -#define gd_42W 30.0000 2.0000 2 +#define gd_42W 100.0000 1.20000 2 ; Backbone dihedral angle -N-CA-C-N- TRP ; -#define gd_43W 80.0000 2.200 3 ; lower k for higher J coupling and more population in intermediate beta region +#define gd_43W 80.0000 0.000 3 ; lower k for higher J coupling and more population in intermediate beta region ; Backbone dihedral angle -C-N-CA-C- TRP ; -#define gd_43Wb -10.000 2.700 2 ; lower k for higher J coupling and more population in intermediate beta region +#define gd_43Wb -150.000 0.800 2 ; lower k for higher J coupling and more population in intermediate beta region ; Backbone dihedral angle -C-N-CA-C- TRP ; -#define gd_44W 68.000 3.0 1 +#define gd_44W -130.000 1.5 1 ; Backbone dihedral angle -C-N-CA-C- TRP ; -#define gd_45W 0.00 6.0 1 +#define gd_45W 0.00 1.0 1 ; Backbone dihedral angle -N-CA-C-N- TRP ; ;;;;;;;;;;;;;;;;;;;; @@ -541,140 +541,140 @@ #define gd_42Q 90.0000 1.5000 2 ; Backbone dihedral angle -N-CA-C-N- GLN ; -#define gd_43Q 15.0000 1.000 3 +#define gd_43Q 15.0000 0.000 3 ; Backbone dihedral angle -C-N-CA-C- GLN ; #define gd_44Q 180.000 2.60 1 ; Backbone dihedral angle -C-N-CA-C- GLN ; -#define gd_45Q 180.000 2.50 1 +#define gd_45Q 180.000 1.00 1 ; Backbone dihedral angle -N-CA-C-N- GLN ; ;;;;;;;;;;;;;;;;;;;; ; LYS ;;;;;;;;;;;;;;;;;;;; -#define gd_42K 100.0000 2.3000 2 +#define gd_42K 100.0000 1.9000 2 ; Backbone dihedral angle -N-CA-C-N- LYS ; -#define gd_43K 30.0000 2.000 3 +#define gd_43K 30.0000 0.000 3 ; Backbone dihedral angle -C-N-CA-C- LYS ; -#define gd_44K 0.000 1.50 1 +#define gd_44K -150.000 2.00 1 ; Backbone dihedral angle -C-N-CA-C- LYS ; -#define gd_44Kb 65.000 1.80 4 +#define gd_44Kb 60.000 0.50 4 ; Backbone dihedral angle -C-N-CA-C- LYS ; -#define gd_45K 0.000 3.0 1 +#define gd_45K 0.000 1.0 1 ; Backbone dihedral angle -N-CA-C-N- LYS ; ;;;;;;;;;;;;;;;;;;;; ; ILE ;;;;;;;;;;;;;;;;;;;; -#define gd_42I 30.0000 2.0000 2 +#define gd_42I 90.0000 2.0000 2 ; Backbone dihedral angle -N-CA-C-N- ILE ; -#define gd_43I 80.0000 2.200 3 ; lower k for higher J coupling and more population in intermediate beta region +#define gd_43I 80.0000 2.400 3 ; lower k for higher J coupling and more population in intermediate beta region ; Backbone dihedral angle -C-N-CA-C- ILE ; -#define gd_43Ib -10.0000 2.700 2 ; lower k for higher J coupling and more population in intermediate beta region +#define gd_43Ib -10.0000 3.000 2 ; lower k for higher J coupling and more population in intermediate beta region ; Backbone dihedral angle -C-N-CA-C- ILE ; -#define gd_44I 68.000 3.0 1 +#define gd_44I 70.000 0.0 1 ; Backbone dihedral angle -C-N-CA-C- ILE ; -#define gd_45I 0.00 6.0 1 +#define gd_45I 180.00 0.4 1 ; Backbone dihedral angle -N-CA-C-N- ILE ; ;;;;;;;;;;;;;;;;;;;; ; VAL ;;;;;;;;;;;;;;;;;;;; -#define gd_42V 30.0000 2.0000 2 +#define gd_42V 100.0000 2.4000 2 ; Backbone dihedral angle -N-CA-C-N- VAL ; -#define gd_43V 95.0000 2.200 3 ; lower k for higher J coupling and more population in intermediate beta region +#define gd_43V 95.0000 0.000 3 ; lower k for higher J coupling and more population in intermediate beta region ; Backbone dihedral angle -C-N-CA-C- VAL ; -#define gd_43Vb -10.0000 2.700 2 ; lower k for higher J coupling and more population in intermediate beta region +#define gd_43Vb -120.0000 1.700 2 ; lower k for higher J coupling and more population in intermediate beta region ; Backbone dihedral angle -C-N-CA-C- VAL ; -#define gd_44V 50.000 3.0 1 +#define gd_44V 100.000 2.5 1 ; Backbone dihedral angle -C-N-CA-C- VAL ; -#define gd_45V 0.00 6.0 1 +#define gd_45V 0.00 0.5 1 ; Backbone dihedral angle -N-CA-C-N- VAL ;;;;;;;;;;;;;;;;;;;; ; PHE ;;;;;;;;;;;;;;;;;;;; -#define gd_42F 30.0000 2.0000 2 +#define gd_42F 100.0000 2.4000 2 ; Backbone dihedral angle -N-CA-C-N- PHE ; -#define gd_43F 80.0000 2.200 3 ; lower k for higher J coupling and more population in intermediate beta region +#define gd_43F 80.0000 0.000 3 ; lower k for higher J coupling and more population in intermediate beta region ; Backbone dihedral angle -C-N-CA-C- PHE ; -#define gd_43Fb -10.0000 2.700 2 ; lower k for higher J coupling and more population in intermediate beta region +#define gd_43Fb -120.0000 1.700 2 ; lower k for higher J coupling and more population in intermediate beta region ; Backbone dihedral angle -C-N-CA-C- PHE ; -#define gd_44F 68.000 3.0 1 +#define gd_44F 100.000 2.5 1 ; Backbone dihedral angle -C-N-CA-C- PHE ; -#define gd_45F 0.00 5.7 1 +#define gd_45F 0.00 0.7 1 ; Backbone dihedral angle -N-CA-C-N- PHE ;;;;;;;;;;;;;;;;;;;; ;SER ;;;;;;;;;;;;;;;;;;;; -#define gd_42S 110.0000 2.9000 2 +#define gd_42S 100.0000 1.9000 2 ; Backbone dihedral angle -N-CA-C-N- SER ; -#define gd_43S -15.0000 2.000 3 +#define gd_43S 30.0000 0.000 3 ; Backbone dihedral angle -C-N-CA-C- SER ; -#define gd_44S -10.000 1.50 1 +#define gd_44S -150.000 2.00 1 ; Backbone dihedral angle -C-N-CA-C- SER ; -#define gd_44Sb 40.000 1.70 4 +#define gd_44Sb 60.000 0.50 4 ; Backbone dihedral angle -C-N-CA-C- SER ; -#define gd_45S 0.00 3.00 1 +#define gd_45S 0.000 1.3 1 ; Backbone dihedral angle -N-CA-C-N- SER ; ;;;;;;;;;;;;;;;;;;;; ;THR ;;;;;;;;;;;;;;;;;;;; -#define gd_42T 30.0000 2.0000 2 +#define gd_42T 100.0000 2.4000 2 ; Backbone dihedral angle -N-CA-C-N- THR ; -#define gd_43T 80.0000 2.200 3 ; lower k for higher J coupling and more population in intermediate beta region +#define gd_43T 80.0000 0.000 3 ; lower k for higher J coupling and more population in intermediate beta region ; Backbone dihedral angle -C-N-CA-C- THR ; -#define gd_43Tb -10.0000 2.700 2 ; lower k for higher J coupling and more population in intermediate beta region +#define gd_43Tb -120.0000 1.700 2 ; lower k for higher J coupling and more population in intermediate beta region ; Backbone dihedral angle -C-N-CA-C- THR ; -#define gd_44T 68.000 3.0 1 -; Backbone dihedral angle -C-N-CA-C- THR +#define gd_44T 100.000 2.5 1 +; Backbone dihedral angle -C-N-CA-C- PHE ; -#define gd_45T 0.00 6.0 1 +#define gd_45T 0.00 0.0 1 ; Backbone dihedral angle -N-CA-C-N- THR ;;;;;;;;;;;;;;;;;;;; ; TYR ;;;;;;;;;;;;;;;;;;;; -#define gd_42Y 30.0000 2.0000 2 +#define gd_42Y 100.0000 2.4000 2 ; Backbone dihedral angle -N-CA-C-N- TYR ; -#define gd_43Y 80.0000 2.200 3 ; lower k for higher J coupling and more population in intermediate beta region +#define gd_43Y 80.0000 0.000 3 ; lower k for higher J coupling and more population in intermediate beta region ; Backbone dihedral angle -C-N-CA-C- TYR ; -#define gd_43Yb -10.0000 2.700 2 ; lower k for higher J coupling and more population in intermediate beta region +#define gd_43Yb -120.0000 1.700 2 ; lower k for higher J coupling and more population in intermediate beta region ; Backbone dihedral angle -C-N-CA-C- TYR ; -#define gd_44Y 68.000 3.0 1 +#define gd_44Y -120.000 1.3 1 ; Backbone dihedral angle -C-N-CA-C- TYR ; -#define gd_45Y 0.00 5.5 1 +#define gd_45Y 0.00 0.7 1 ; Backbone dihedral angle -N-CA-C-N- TYR @@ -685,22 +685,22 @@ #define gd_48G 180.0 5.0 2 ; Backbone dihedral angle -N-CA-C-N GLY ; -#define gd_49G 180 5.0 1 +#define gd_49G 180 3.0 1 ; Backbone dihedral angle -C-N-CA-C GLY ; -#define gd_51G 180 2.5 1 +#define gd_51G 180 1.0 1 ; Backbone dihedral angle -N-CA-C-N GLY ; ;;;;;;;;;;;;;;;;;;;; ;PRO ;;;;;;;;;;;;;;;;;;;; -#define gd_52P 150.0000 4.0000 2 +#define gd_52P 180.0000 5.0000 2 ; Backbone dihedral angle -N-CA-C-N PRO ; #define gd_53P 0.0000 4.000 4 ; Backbone dihedral angle -C-N-CA-C PRO ; -#define gd_55P 180.0000 0.40 1 +#define gd_55P 180.0000 0.80 1 ; Backbone dihedral angle -N-CA-C-N PRO ; #define gd_56P 180.000 31.0 2