From 12504c6502dcacd8d9c81c5f618b9ed2dba51c4a Mon Sep 17 00:00:00 2001 From: Bruno Stegani Date: Mon, 16 Dec 2024 11:48:05 +0100 Subject: [PATCH 1/3] changed H name from HN to H and removed H definition in PRO --- multi-ego-basic.ff/aminoacids.hdb | 45 +++--- multi-ego-basic.ff/aminoacids.n.tdb | 2 +- multi-ego-basic.ff/aminoacids.rtp | 214 ++++++++++++++-------------- 3 files changed, 127 insertions(+), 134 deletions(-) diff --git a/multi-ego-basic.ff/aminoacids.hdb b/multi-ego-basic.ff/aminoacids.hdb index 6ae4aef8..039c4fbd 100644 --- a/multi-ego-basic.ff/aminoacids.hdb +++ b/multi-ego-basic.ff/aminoacids.hdb @@ -1,65 +1,62 @@ ALA 1 -1 1 HN N -C CA +1 1 H N -C CA ARG 1 -1 1 HN N -C CA +1 1 H N -C CA ASN 1 -1 1 HN N -C CA +1 1 H N -C CA ASP 1 -1 1 HN N -C CA +1 1 H N -C CA CYS 1 -1 1 HN N -C CA +1 1 H N -C CA CYS2 1 -1 1 HN N -C CA +1 1 H N -C CA GLN 1 -1 1 HN N -C CA +1 1 H N -C CA GLU 1 -1 1 HN N -C CA +1 1 H N -C CA GLY 1 -1 1 HN N -C CA +1 1 H N -C CA HYS 1 -1 1 HN N -C CA +1 1 H N -C CA ILE 1 -1 1 HN N -C CA +1 1 H N -C CA LEU 1 -1 1 HN N -C CA +1 1 H N -C CA LYS 1 -1 1 HN N -C CA +1 1 H N -C CA MET 1 -1 1 HN N -C CA +1 1 H N -C CA PHE 1 -1 1 HN N -C CA - -PRO 1 -1 1 HN N -C CA +1 1 H N -C CA SER 1 -1 1 HN N -C CA +1 1 H N -C CA THR 1 -1 1 HN N -C CA +1 1 H N -C CA TRP 1 -1 1 HN N -C CA +1 1 H N -C CA TYR 1 -1 1 HN N -C CA +1 1 H N -C CA NME 1 -1 1 HN N -C CA +1 1 H N -C CA VAL 1 -1 1 HN N -C CA +1 1 H N -C CA diff --git a/multi-ego-basic.ff/aminoacids.n.tdb b/multi-ego-basic.ff/aminoacids.n.tdb index 9c553cae..e4617a28 100644 --- a/multi-ego-basic.ff/aminoacids.n.tdb +++ b/multi-ego-basic.ff/aminoacids.n.tdb @@ -2,7 +2,7 @@ [ replace ] N NL 17.0067 0.000 ; weight and charge include the 3 hydrogens [ delete ] - HN + H [ PRO-NH2+ ] diff --git a/multi-ego-basic.ff/aminoacids.rtp b/multi-ego-basic.ff/aminoacids.rtp index 505bd52c..f517a61f 100644 --- a/multi-ego-basic.ff/aminoacids.rtp +++ b/multi-ego-basic.ff/aminoacids.rtp @@ -27,17 +27,17 @@ [ NME ] [ atoms ] N N 0.000 0 - HN H 0.000 0 + H H 0.000 0 CA CH3 0.000 0 [ bonds ] N CA gb_21 - N HN gb_2 + N H gb_2 [ angles ] -C N CA ga_31 - HN N CA ga_18 - -C N HN ga_32 + H N CA ga_18 + -C N H ga_32 [ impropers ] - N -C CA HN gi_1 + N -C CA H gi_1 [ dihedrals ] -CA -C N CA gd_14 @@ -56,13 +56,13 @@ [ ALA ] [ atoms ] N N 0.000 0 - HN H 0.000 0 + H H 0.000 0 CA CAH 0.000 0 CB CH3 0.000 0 C C 0.000 0 O O 0.000 0 [ bonds ] - N HN gb_2 + N H gb_2 N CA gb_21 CA CB gb_27 CA C gb_27 @@ -70,9 +70,9 @@ C +N gb_10 [ angles ] ; ai aj ak gromos type - -C N HN ga_32 + -C N H ga_32 -C N CA ga_31 - HN N CA ga_18 + H N CA ga_18 N CA CB ga_13 N CA C ga_13 CB CA C ga_13 @@ -81,7 +81,7 @@ O C +N ga_33 [ impropers ] ; ai aj ak al gromos type - N -C CA HN gi_1 + N -C CA H gi_1 CA N C CB gi_2 C CA +N O gi_1 [ dihedrals ] @@ -95,7 +95,7 @@ [ ARG ] [ atoms ] N N 0.000 0 - HN H 0.000 0 + H H 0.000 0 CA CAH 0.000 0 CB CH2 0.000 0 CG CH2 0.000 0 @@ -108,7 +108,7 @@ O O 0.000 0 [ bonds ] N CA gb_21 - N HN gb_2 + N H gb_2 CA CB gb_27 CA C gb_27 CB CG gb_27 @@ -121,9 +121,9 @@ C +N gb_10 [ angles ] ; ai aj ak gromos type - -C N HN ga_32 + -C N H ga_32 -C N CA ga_31 - HN N CA ga_18 + H N CA ga_18 N CA CB ga_13 N CA C ga_13 CB CA C ga_13 @@ -139,7 +139,7 @@ O C +N ga_33 [ impropers ] ; ai aj ak al gromos type - N -C CA HN gi_1 + N -C CA H gi_1 CA N C CB gi_2 CZ NH1 NH2 NE gi_1 C CA +N O gi_1 @@ -159,7 +159,7 @@ [ ASN ] [ atoms ] N N 0.000 0 - HN H 0.000 0 + H H 0.000 0 CA CAH 0.000 0 CB CH2 0.000 0 CG C 0.000 0 @@ -168,7 +168,7 @@ C C 0.000 0 O O 0.000 0 [ bonds ] - N HN gb_2 + N H gb_2 N CA gb_21 CA CB gb_27 CA C gb_27 @@ -179,9 +179,9 @@ C +N gb_10 [ angles ] ; ai aj ak gromos type - -C N HN ga_32 + -C N H ga_32 -C N CA ga_31 - HN N CA ga_18 + H N CA ga_18 N CA CB ga_13 N CA C ga_13 CB CA C ga_13 @@ -194,7 +194,7 @@ O C +N ga_33 [ impropers ] ; ai aj ak al gromos type - N -C CA HN gi_1 + N -C CA H gi_1 CA N C CB gi_2 CG OD1 ND2 CB gi_1 C CA +N O gi_1 @@ -211,7 +211,7 @@ [ ASP ] [ atoms ] N N 0.000 0 - HN H 0.000 0 + H H 0.000 0 CA CAH 0.000 0 CB CH2 0.000 0 CG C 0.000 0 @@ -221,7 +221,7 @@ O O 0.000 0 [ bonds ] N CA gb_21 - N HN gb_2 + N H gb_2 CA CB gb_27 CA C gb_27 CB CG gb_27 @@ -231,9 +231,9 @@ C +N gb_10 [ angles ] ; ai aj ak gromos type - -C N HN ga_32 + -C N H ga_32 -C N CA ga_31 - HN N CA ga_18 + H N CA ga_18 N CA CB ga_13 N CA C ga_13 CB CA C ga_13 @@ -246,7 +246,7 @@ O C +N ga_33 [ impropers ] ; ai aj ak al gromos type - N -C CA HN gi_1 + N -C CA H gi_1 CA N C CB gi_2 CG OD1 OD2 CB gi_1 C CA +N O gi_1 @@ -263,7 +263,7 @@ [ CYS ] [ atoms ] N N 0.000 0 - HN H 0.000 0 + H H 0.000 0 CA CAH 0.000 0 CB CH2 0.000 0 SG S 0.000 0 @@ -271,7 +271,7 @@ O O 0.000 0 [ bonds ] N CA gb_21 - N HN gb_2 + N H gb_2 CA CB gb_27 CA C gb_27 CB SG gb_32 @@ -279,9 +279,9 @@ C +N gb_10 [ angles ] ; ai aj ak gromos type - -C N HN ga_32 + -C N H ga_32 -C N CA ga_31 - HN N CA ga_18 + H N CA ga_18 N CA CB ga_13 N CA C ga_13 CB CA C ga_13 @@ -291,7 +291,7 @@ O C +N ga_33 [ impropers ] ; ai aj ak al gromos type - N -C CA HN gi_1 + N -C CA H gi_1 CA N C CB gi_2 C CA +N O gi_1 [ dihedrals ] @@ -306,7 +306,7 @@ [ CYS2 ] [ atoms ] N N 0.000 0 - HN H 0.000 0 + H H 0.000 0 CA CAH 0.000 0 CB CH2 0.000 0 SG S 0.000 0 @@ -314,7 +314,7 @@ O O 0.000 0 [ bonds ] N CA gb_21 - N HN gb_2 + N H gb_2 CA CB gb_27 CA C gb_27 CB SG gb_32 @@ -322,9 +322,9 @@ C +N gb_10 [ angles ] ; ai aj ak gromos type - -C N HN ga_32 + -C N H ga_32 -C N CA ga_31 - HN N CA ga_18 + H N CA ga_18 N CA CB ga_13 N CA C ga_13 CB CA C ga_13 @@ -334,7 +334,7 @@ O C +N ga_33 [ impropers ] ; ai aj ak al gromos type - N -C CA HN gi_1 + N -C CA H gi_1 CA N C CB gi_2 C CA +N O gi_1 [ dihedrals ] @@ -349,7 +349,7 @@ [ GLN ] [ atoms ] N N 0.000 0 - HN H 0.000 0 + H H 0.000 0 CA CAH 0.000 0 CB CH2 0.000 0 CG CH2 0.000 0 @@ -360,7 +360,7 @@ O O 0.000 0 [ bonds ] N CA gb_21 - N HN gb_2 + N H gb_2 CA CB gb_27 CA C gb_27 CB CG gb_27 @@ -371,9 +371,9 @@ C +N gb_10 [ angles ] ; ai aj ak gromos type - -C N HN ga_32 + -C N H ga_32 -C N CA ga_31 - HN N CA ga_18 + H N CA ga_18 N CA CB ga_13 N CA C ga_13 CB CA C ga_13 @@ -387,7 +387,7 @@ O C +N ga_33 [ impropers ] ; ai aj ak al gromos type - N -C CA HN gi_1 + N -C CA H gi_1 CA N C CB gi_2 CD OE1 NE2 CG gi_1 C CA +N O gi_1 @@ -405,7 +405,7 @@ [ GLU ] [ atoms ] N N 0.000 0 - HN H 0.000 0 + H H 0.000 0 CA CAH 0.000 0 CB CH2 0.000 0 CG CH2 0.000 0 @@ -416,7 +416,7 @@ O O 0.000 0 [ bonds ] N CA gb_21 - N HN gb_2 + N H gb_2 CA CB gb_27 CA C gb_27 CB CG gb_27 @@ -427,9 +427,9 @@ C +N gb_10 [ angles ] ; ai aj ak gromos type - -C N HN ga_32 + -C N H ga_32 -C N CA ga_31 - HN N CA ga_18 + H N CA ga_18 N CA CB ga_13 N CA C ga_13 CB CA C ga_13 @@ -443,7 +443,7 @@ O C +N ga_33 [ impropers ] ; ai aj ak al gromos type - N -C CA HN gi_1 + N -C CA H gi_1 CA N C CB gi_2 CD OE1 OE2 CG gi_1 C CA +N O gi_1 @@ -461,29 +461,29 @@ [ GLY ] [ atoms ] N N 0.000 0 - HN H 0.000 0 + H H 0.000 0 CA CH2 0.000 0 C C 0.000 0 O O 0.000 0 [ bonds ] N CA gb_21 - N HN gb_2 + N H gb_2 CA C gb_27 C O gb_5 C +N gb_10 [ angles ] ; ai aj ak gromos type - -C N HN ga_32 + -C N H ga_32 -C N CA ga_31 N CA C ga_13 - HN N CA ga_18 + H N CA ga_18 CA C O ga_30 CA C +N ga_19 O C +N ga_33 [ impropers ] ; ai aj ak al gromos type C CA +N O gi_1 - N -C CA HN gi_1 + N -C CA H gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_14 @@ -494,7 +494,7 @@ [ HIS ] [ atoms ] N N 0.000 0 - HN H 0.000 0 + H H 0.000 0 CA CAH 0.000 0 CB CH2 0.000 0 CG C 0.000 0 @@ -506,7 +506,7 @@ O O 0.000 0 [ bonds ] N CA gb_21 - N HN gb_2 + N H gb_2 CA CB gb_27 CA C gb_27 CB CG gb_27 @@ -519,9 +519,9 @@ C +N gb_10 [ angles ] ; ai aj ak gromos type - -C N HN ga_32 + -C N H ga_32 -C N CA ga_31 - HN N CA ga_18 + H N CA ga_18 N CA CB ga_13 N CA C ga_13 CB CA C ga_13 @@ -539,7 +539,7 @@ [ impropers ] ; ai aj ak al gromos type CA N C CB gi_2 - N -C CA HN gi_1 + N -C CA H gi_1 CG ND1 CD2 CB gi_1 CG ND1 CE1 NE2 gi_1 CG CD2 NE2 CE1 gi_1 @@ -560,7 +560,7 @@ [ ILE ] [ atoms ] N N 0.000 0 - HN H 0.000 0 + H H 0.000 0 CA CAH 0.000 0 CB CH1 0.000 0 CG1 CH2 0.000 0 @@ -570,7 +570,7 @@ O O 0.000 0 [ bonds ] N CA gb_21 - N HN gb_2 + N H gb_2 CA CB gb_27 CA C gb_27 CB CG1 gb_27 @@ -580,9 +580,9 @@ C +N gb_10 [ angles ] ; ai aj ak gromos type - -C N HN ga_32 + -C N H ga_32 -C N CA ga_31 - HN N CA ga_18 + H N CA ga_18 N CA CB ga_13 N CA C ga_13 CB CA C ga_13 @@ -596,7 +596,7 @@ [ impropers ] ; ai aj ak al gromos type CA N C CB gi_2 - N -C CA HN gi_1 + N -C CA H gi_1 CB CG1 CG2 CA gi_2 C CA +N O gi_1 [ dihedrals ] @@ -612,7 +612,7 @@ [ LEU ] [ atoms ] N N 0.000 0 - HN H 0.000 0 + H H 0.000 0 CA CAH 0.000 0 CB CH2 0.000 0 CG CH1 0.000 0 @@ -622,7 +622,7 @@ O O 0.000 0 [ bonds ] N CA gb_21 - N HN gb_2 + N H gb_2 CA CB gb_27 CA C gb_27 CB CG gb_27 @@ -632,9 +632,9 @@ C +N gb_10 [ angles ] ; ai aj ak gromos type - -C N HN ga_32 + -C N H ga_32 -C N CA ga_31 - HN N CA ga_18 + H N CA ga_18 N CA CB ga_13 N CA C ga_13 CB CA C ga_13 @@ -648,7 +648,7 @@ [ impropers ] ; ai aj ak al gromos type CA N C CB gi_2 - N -C CA HN gi_1 + N -C CA H gi_1 CB CD1 CD2 CG gi_2 C CA +N O gi_1 [ dihedrals ] @@ -664,7 +664,7 @@ [ LYS ] [ atoms ] N N 0.000 0 - HN H 0.000 0 + H H 0.000 0 CA CAH 0.000 0 CB CH2 0.000 0 CG CH2 0.000 0 @@ -675,7 +675,7 @@ O O 0.000 0 [ bonds ] N CA gb_21 - N HN gb_2 + N H gb_2 CA CB gb_27 CA C gb_27 CB CG gb_27 @@ -686,9 +686,9 @@ C +N gb_10 [ angles ] ; ai aj ak gromos type - -C N HN ga_32 + -C N H ga_32 -C N CA ga_31 - HN N CA ga_18 + H N CA ga_18 N CA CB ga_13 N CA C ga_13 CB CA C ga_13 @@ -702,7 +702,7 @@ [ impropers ] ; ai aj ak al gromos type CA N C CB gi_2 - N -C CA HN gi_1 + N -C CA H gi_1 C CA +N O gi_1 [ dihedrals ] ; ai aj ak al gromos type @@ -719,7 +719,7 @@ [ MET ] [ atoms ] N N 0.000 0 - HN H 0.000 0 + H H 0.000 0 CA CAH 0.000 0 CB CH2 0.000 0 CG CH2 0.000 0 @@ -729,7 +729,7 @@ O O 0.000 0 [ bonds ] N CA gb_21 - N HN gb_2 + N H gb_2 CA CB gb_27 CA C gb_27 CB CG gb_27 @@ -739,9 +739,9 @@ C +N gb_10 [ angles ] ; ai aj ak gromos type - -C N HN ga_32 + -C N H ga_32 -C N CA ga_31 - HN N CA ga_18 + H N CA ga_18 N CA CB ga_13 N CA C ga_13 CB CA C ga_13 @@ -754,7 +754,7 @@ [ impropers ] ; ai aj ak al gromos type CA N C CB gi_2 - N -C CA HN gi_1 + N -C CA H gi_1 C CA +N O gi_1 [ dihedrals ] ; ai aj ak al gromos type @@ -770,7 +770,7 @@ [ PHE ] [ atoms ] N N 0.000 0 - HN H 0.000 0 + H H 0.000 0 CA CAH 0.000 0 CB CH2 0.000 0 CG CH 0.000 0 @@ -783,7 +783,7 @@ O O 0.000 0 [ bonds ] N CA gb_21 - N HN gb_2 + N H gb_2 CA CB gb_27 CA C gb_27 CB CG gb_27 @@ -797,9 +797,9 @@ C +N gb_10 [ angles ] ; ai aj ak gromos type - -C N HN ga_32 + -C N H ga_32 -C N CA ga_31 - HN N CA ga_18 + H N CA ga_18 N CA CB ga_13 N CA C ga_13 CB CA C ga_13 @@ -818,7 +818,7 @@ [ impropers ] ; ai aj ak al gromos type CA N C CB gi_2 - N -C CA HN gi_1 + N -C CA H gi_1 CG CD1 CD2 CB gi_1 CG CD1 CE1 CZ gi_1 CG CD2 CE2 CZ gi_1 @@ -840,7 +840,6 @@ [ PRO ] [ atoms ] N N 0.000 0 - HN H 0.000 0 CA CAH 0.000 0 CB CH2r 0.000 0 CG CH2r 0.000 0 @@ -849,7 +848,6 @@ O O 0.000 0 [ bonds ] N CA gb_21 - N HN gb_2 N CD gb_21 CA CB gb_27 CA C gb_27 @@ -859,9 +857,7 @@ C +N gb_10 [ angles ] ; ai aj ak gromos type - -C N HN ga_32 -C N CA ga_31 - HN N CA ga_18 -C N CD ga_31 CA N CD ga_21 N CA CB ga_13 @@ -893,7 +889,7 @@ [ SER ] [ atoms ] N N 0.000 0 - HN H 0.000 0 + H H 0.000 0 CA CAH 0.000 0 CB CH2 0.000 0 OG OA 0.000 0 @@ -901,7 +897,7 @@ O O 0.000 0 [ bonds ] N CA gb_21 - N HN gb_2 + N H gb_2 CA CB gb_27 CA C gb_27 CB OG gb_18 @@ -909,9 +905,9 @@ C +N gb_10 [ angles ] ; ai aj ak gromos type - -C N HN ga_32 + -C N H ga_32 -C N CA ga_31 - HN N CA ga_18 + H N CA ga_18 N CA CB ga_13 N CA C ga_13 CB CA C ga_13 @@ -922,7 +918,7 @@ [ impropers ] ; ai aj ak al gromos type CA N C CB gi_2 - N -C CA HN gi_1 + N -C CA H gi_1 C CA +N O gi_1 [ dihedrals ] ; ai aj ak al gromos type @@ -936,7 +932,7 @@ [ THR ] [ atoms ] N N 0.000 0 - HN H 0.000 0 + H H 0.000 0 CA CAH 0.000 0 CB CH1 0.000 0 OG1 OA 0.000 0 @@ -945,7 +941,7 @@ O O 0.000 0 [ bonds ] N CA gb_21 - N HN gb_2 + N H gb_2 CA CB gb_27 CA C gb_27 CB OG1 gb_18 @@ -954,9 +950,9 @@ C +N gb_10 [ angles ] ; ai aj ak gromos type - -C N HN ga_32 + -C N H ga_32 -C N CA ga_31 - HN N CA ga_18 + H N CA ga_18 N CA CB ga_13 N CA C ga_13 CB CA C ga_13 @@ -969,7 +965,7 @@ [ impropers ] ; ai aj ak al gromos type CA N C CB gi_2 - N -C CA HN gi_1 + N -C CA H gi_1 CB OG1 CG2 CA gi_2 C CA +N O gi_1 [ dihedrals ] @@ -984,7 +980,7 @@ [ TRP ] [ atoms ] N N 0.000 0 - HN H 0.000 0 + H H 0.000 0 CA CAH 0.000 0 CB CH2 0.000 0 CG CH 0.000 0 @@ -1000,7 +996,7 @@ O O 0.000 0 [ bonds ] N CA gb_21 - N HN gb_2 + N H gb_2 CA CB gb_27 CA C gb_27 CB CG gb_27 @@ -1018,9 +1014,9 @@ C +N gb_10 [ angles ] ; ai aj ak gromos type - -C N HN ga_32 + -C N H ga_32 -C N CA ga_31 - HN N CA ga_18 + H N CA ga_18 N CA CB ga_13 N CA C ga_13 CB CA C ga_13 @@ -1046,7 +1042,7 @@ [ impropers ] ; ai aj ak al gromos type CA N C CB gi_2 - N -C CA HN gi_1 + N -C CA H gi_1 CG CD1 CD2 CB gi_1 CG CD1 NE1 CE2 gi_1 CG CD2 CE2 NE1 gi_1 @@ -1075,7 +1071,7 @@ [ TYR ] [ atoms ] N N 0.000 0 - HN H 0.000 0 + H H 0.000 0 CA CAH 0.000 0 CB CH2 0.000 0 CG CH 0.000 0 @@ -1089,7 +1085,7 @@ O O 0.000 0 [ bonds ] N CA gb_21 - N HN gb_2 + N H gb_2 CA CB gb_27 CA C gb_27 CB CG gb_27 @@ -1104,9 +1100,9 @@ C +N gb_10 [ angles ] ; ai aj ak gromos type - -C N HN ga_32 + -C N H ga_32 -C N CA ga_31 - HN N CA ga_18 + H N CA ga_18 N CA CB ga_13 N CA C ga_13 CB CA C ga_13 @@ -1127,7 +1123,7 @@ [ impropers ] ; ai aj ak al gromos type CA N C CB gi_2 - N -C CA HN gi_1 + N -C CA H gi_1 CG CD1 CD2 CB gi_1 CG CD1 CE1 CZ gi_1 CG CD2 CE2 CZ gi_1 @@ -1150,7 +1146,7 @@ [ VAL ] [ atoms ] N N 0.000 0 - HN H 0.000 0 + H H 0.000 0 CA CAH 0.000 0 CB CH1 0.000 0 CG1 CH3 0.000 0 @@ -1159,7 +1155,7 @@ O O 0.000 0 [ bonds ] N CA gb_21 - N HN gb_2 + N H gb_2 CA CB gb_27 CA C gb_27 CB CG1 gb_27 @@ -1168,9 +1164,9 @@ C +N gb_10 [ angles ] ; ai aj ak gromos type - -C N HN ga_32 + -C N H ga_32 -C N CA ga_31 - HN N CA ga_18 + H N CA ga_18 N CA CB ga_13 N CA C ga_13 CB CA C ga_13 @@ -1182,7 +1178,7 @@ O C +N ga_33 [ impropers ] ; ai aj ak al gromos type - N -C CA HN gi_1 + N -C CA H gi_1 CA N C CB gi_2 CA CG1 CG2 CB gi_2 C CA +N O gi_1 From 27b822d590ab947188f25f6e25c71000639b0c4c Mon Sep 17 00:00:00 2001 From: Bruno Stegani Date: Mon, 16 Dec 2024 12:04:55 +0100 Subject: [PATCH 2/3] HYS --> HIS --- multi-ego-basic.ff/aminoacids.hdb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/multi-ego-basic.ff/aminoacids.hdb b/multi-ego-basic.ff/aminoacids.hdb index 039c4fbd..9e4f1fb4 100644 --- a/multi-ego-basic.ff/aminoacids.hdb +++ b/multi-ego-basic.ff/aminoacids.hdb @@ -25,7 +25,7 @@ GLU 1 GLY 1 1 1 H N -C CA -HYS 1 +HIS 1 1 1 H N -C CA ILE 1 From 4467ac8039d2f4b684db9cbb406558982804614e Mon Sep 17 00:00:00 2001 From: Bruno Stegani Date: Mon, 16 Dec 2024 12:15:57 +0100 Subject: [PATCH 3/3] makemat and cmdata modifications for bkbn H --- tools/cmdata/main.cpp | 9 ++++++--- tools/cmdata/src/cmdata/cmdata.hpp | 14 ++++++++------ tools/make_mat/make_mat.py | 26 +++++++++++++++++++------- 3 files changed, 33 insertions(+), 16 deletions(-) diff --git a/tools/cmdata/main.cpp b/tools/cmdata/main.cpp index e10ab611..61b6fe68 100644 --- a/tools/cmdata/main.cpp +++ b/tools/cmdata/main.cpp @@ -18,9 +18,9 @@ int main(int argc, const char** argv) double cutoff = 0.75, mol_cutoff = 6.0; int nskip = 0, num_threads = 1, mol_threads = -1, dt = 0; float t_begin = 0.0, t_end = -1.0; - char *p_traj_path = NULL, *p_top_path = NULL, *p_mode = NULL, *p_weights_path = NULL; + char *p_traj_path = NULL, *p_top_path = NULL, *p_mode = NULL,*p_bkbn_H = NULL, *p_weights_path = NULL; char *p_out_prefix = NULL; - std::string traj_path, top_path, mode, weights_path; + std::string traj_path, top_path, mode, weights_path, bkbn_H; std::string out_prefix; int *p_nopbc = NULL; int *p_res = NULL; @@ -42,6 +42,7 @@ int main(int argc, const char** argv) {"num_threads", '\0', POPT_ARG_INT | POPT_ARGFLAG_OPTIONAL, &num_threads, 0, "Number of threads", "INT"}, {"mol_threads", '\0', POPT_ARG_INT | POPT_ARGFLAG_OPTIONAL, &mol_threads, 0, "Number of molecule threads", "INT"}, {"mode", '\0', POPT_ARG_STRING | POPT_ARGFLAG_OPTIONAL, &p_mode, 0, "Mode of operation", "STRING"}, + {"bkbn_H", '\0', POPT_ARG_STRING | POPT_ARGFLAG_OPTIONAL, &p_bkbn_H, 0, "Backbone H name", "STRING"}, {"weights", '\0', POPT_ARG_STRING | POPT_ARGFLAG_OPTIONAL, &p_weights_path, 0, "Weights file", "FILE"}, {"no_pbc", '\0', POPT_ARG_NONE | POPT_ARGFLAG_OPTIONAL, &p_nopbc, 0, "Ignore pbcs", 0}, POPT_TABLEEND @@ -66,7 +67,9 @@ int main(int argc, const char** argv) traj_path = std::string(p_traj_path); top_path = std::string(p_top_path); + //bkbn_H = std::string(p_bkbn_H); mode = p_mode ? std::string(p_mode) : std::string("intra+same+cross"); + bkbn_H = p_bkbn_H ? std::string(p_bkbn_H) : std::string("H"); if ( p_weights_path != NULL ) weights_path = std::string(p_weights_path); if ( p_out_prefix != NULL ) out_prefix = std::string(p_out_prefix); if ( p_nopbc != NULL ) nopbc = true; @@ -151,7 +154,7 @@ int main(int argc, const char** argv) cmdata::CMData cmdata( top_path, traj_path, cutoff, mol_cutoff, nskip, num_threads, mol_threads, dt, - mode, weights_path, nopbc, t_begin, t_end + mode, bkbn_H, weights_path, nopbc, t_begin, t_end ); cmdata.run(); cmdata.process_data(); diff --git a/tools/cmdata/src/cmdata/cmdata.hpp b/tools/cmdata/src/cmdata/cmdata.hpp index 18ce8ba3..4fd2cccb 100644 --- a/tools/cmdata/src/cmdata/cmdata.hpp +++ b/tools/cmdata/src/cmdata/cmdata.hpp @@ -59,6 +59,7 @@ class CMData std::vector inv_num_mol_unique_; std::vector inv_num_mol_; + std::string bkbn_H_; // weights fields double weights_sum_; std::string weights_path_; @@ -123,7 +124,7 @@ class CMData cmdata_matrix &intram_mat_density_, cmdata_matrix &interm_same_mat_density_, std::vector> &frame_cross_mat_, std::vector> &frame_cross_mutex_, cmdata_matrix &interm_cross_mat_density_, cmdata::parallel::Semaphore &semaphore_, const std::function &f_intra_mol_, const std::function &f_inter_mol_same_, - const std::function &f_inter_mol_cross_, double weight + const std::function &f_inter_mol_cross_, double weight, std::string bkbn_H_ ) { semaphore_.acquire(); @@ -163,7 +164,7 @@ class CMData { std::size_t a_j = 0; mtopGetAtomAndResidueName(*mtop_, ii, &molb, &atomname, nullptr, nullptr, nullptr); - if (atomname[0] == 'H') + if (atomname[0] == 'H' && atomname != bkbn_H_) { a_i++; continue; @@ -172,7 +173,7 @@ class CMData for (std::size_t jj = mols_.block(j).begin(); jj < mols_.block(j).end(); jj++) { mtopGetAtomAndResidueName(*mtop_, jj, &molb, &atomname, nullptr, nullptr, nullptr); - if (atomname[0] == 'H') + if (atomname[0] == 'H' && atomname != bkbn_H_) { a_j++; continue; @@ -235,10 +236,10 @@ class CMData CMData( const std::string &top_path, const std::string &traj_path, double cutoff, double mol_cutoff, int nskip, int num_threads, int num_mol_threads, - int dt, const std::string &mode, const std::string &weights_path, + int dt, const std::string &mode, const std::string &bkbn_H, const std::string &weights_path, bool no_pbc, float t_begin, float t_end ) : cutoff_(cutoff), mol_cutoff_(mol_cutoff), nskip_(nskip), num_threads_(num_threads), num_mol_threads_(num_mol_threads), - mode_(mode), weights_path_(weights_path), + mode_(mode), bkbn_H_(bkbn_H), weights_path_(weights_path), no_pbc_(no_pbc), dt_(dt), t_begin_(t_begin), t_end_(t_end) { bool bTop_; @@ -248,6 +249,7 @@ class CMData int natoms; pbcType_ = read_tpx(top_path.c_str(), nullptr, boxtop_, &natoms, nullptr, nullptr, mtop_); + //const std::string bkbn_H_ = "HN"; if (no_pbc_) { pbc_ = nullptr; @@ -666,7 +668,7 @@ class CMData std::cref(density_bins_), mcut2_, xcm_, mols_, mtop_, std::ref(frame_same_mat_), std::ref(frame_same_mutex_), std::ref(intram_mat_density_), std::ref(interm_same_mat_density_), std::ref(frame_cross_mat_), std::ref(frame_cross_mutex_), std::ref(interm_cross_mat_density_), std::ref(semaphore_), std::cref(f_intra_mol_), - std::cref(f_inter_mol_same_), std::cref(f_inter_mol_cross_), weight); + std::cref(f_inter_mol_same_), std::cref(f_inter_mol_cross_), weight, bkbn_H_); /* end molecule thread */ } /* join molecule threads */ diff --git a/tools/make_mat/make_mat.py b/tools/make_mat/make_mat.py index a24aef00..a6bd0f7d 100644 --- a/tools/make_mat/make_mat.py +++ b/tools/make_mat/make_mat.py @@ -565,13 +565,22 @@ def main_routine(mol_i, mol_j, topology_mego, topology_ref, molecules_name, pref protein_ref_j = topology_ref.molecules[list(topology_ref.molecules.keys())[mol_j - 1]][0] original_size_j = len(protein_ref_j.atoms) - - protein_ref_indices_i = np.array([i + 1 for i in range(len(protein_ref_i.atoms)) if protein_ref_i[i].element_name != "H"]) - protein_ref_indices_j = np.array([i + 1 for i in range(len(protein_ref_j.atoms)) if protein_ref_j[i].element_name != "H"]) - - protein_ref_i = [a for a in protein_ref_i.atoms if a.element_name != "H"] - protein_ref_j = [a for a in protein_ref_j.atoms if a.element_name != "H"] - + # print(dir(protein_ref_i[0])) + # print(dir(protein_ref_i.atoms)) + # print((protein_ref_i[0].name)) + # print(args.bkbn_H) + # print(np.array([ protein_ref_i[i].name for i in range(len(protein_ref_i.atoms)) if (protein_ref_i[i].element_name != "H" or protein_ref_i[i].name == args.bkbn_H)])) + # print(np.array([ protein_ref_i[i].element_name for i in range(len(protein_ref_i.atoms)) ])) + #exit() + protein_ref_indices_i = np.array([i + 1 for i in range(len(protein_ref_i.atoms)) if (protein_ref_i[i].element_name != "H" or protein_ref_i[i].name == args.bkbn_H)]) + protein_ref_indices_j = np.array([i + 1 for i in range(len(protein_ref_j.atoms)) if (protein_ref_i[i].element_name != "H" or protein_ref_i[i].name == args.bkbn_H)]) + + protein_ref_i = [a for a in protein_ref_i.atoms if (a.element_name != "H" or a.name == args.bkbn_H)] + protein_ref_j = [a for a in protein_ref_j.atoms if(a.element_name != "H" or a.name == args.bkbn_H)] + + print(len(protein_ref_i)) + print("\n\n") + #print(len(protein_mego_i)) sorter_i = [str(x.residue.number) + map_if_exists(x.name) for x in protein_ref_i] sorter_mego_i = [str(x.residue.number) + x.name for x in protein_mego_i] @@ -838,6 +847,9 @@ def main_routine(mol_i, mol_j, topology_mego, topology_ref, molecules_name, pref parser.add_argument( "--mode", help="Sets the caculation to be intra/same/cross for histograms processing", default="intra+same+cross" ) + parser.add_argument( + "--bkbn_H", help="Name of backbone hydrogen (default H, charmm HN)", default="H" + ) parser.add_argument("--out", default="./", help="""Sets the output path""") parser.add_argument( "--out_name",