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From: Gordon Richard Chalmers <gordoncs.uga.edu>

Date: Sun, 29 Nov 2020 03:43:05 +0000

I have a question about gaps that I will be solving

soon. Why does my Matlab protein structure software

produce this when using pdb4amber:

I am not new to amber, and the coordinates are good in

this file, which I made by rotating phi/psi/chi angles from

a linear structure. Nonplanar because I used dihedral

angles from the PDB model 1 structure to rotate about

the bonds from a linear structure, with amino acid coordinates

from the Cyana lib. There is no issue with PDB files, only

when I rotate angles and create a new pdb file which is in the

format, which I used pdb4format also to check the indentations.

I attached the initial linear peptide 2L3W 143 residue chain which

does not load correctly in pymol although the coordinates are

correct and can be seen. I am using the linear structure to find

the general one by rotating about dihedral bonds phi/psi and chi.

Simply rotating bonds should not cause problems in a pdb file if

done correctly, and certainly not produce gaps; I have checked

bond distances in my 'rotated' protein model. Attaching the

pdb files exceeds the Amber reflector memory limit.

(base) gordon.pop-os:~/Desktop/protein_program$ pdb4amber -i protein_2L3W_nonplanar.pdb -o protein_2L3W_nonplanar_nohyd.pdb --nohyd

==================================================

Summary of pdb4amber for: protein_2L3W_nonplanar.pdb

===================================================

----------Chains

The following (original) chains have been found:

A

---------- Alternate Locations (Original Residues!))

The following residues had alternate locations:

None

-----------Non-standard-resnames

---------- Gaps (Renumbered Residues!)

gap of 3.180778 A between MET 1 and PRO 2

gap of 3.532217 A between PRO 2 and LEU 3

gap of 2.706905 A between LEU 3 and GLU 4

gap of 2.701192 A between GLU 4 and TRP 5

gap of 2.716848 A between TRP 5 and ARG 6

gap of 2.755144 A between ARG 6 and ALA 7

gap of 2.804152 A between ALA 7 and GLY 8

gap of 2.709739 A between GLY 8 and ALA 9

gap of 2.704501 A between ALA 9 and SER 10

gap of 2.732872 A between SER 10 and SER 11

gap of 2.723781 A between SER 11 and ASP 12

gap of 2.719689 A between ASP 12 and GLU 13

gap of 2.720244 A between GLU 13 and ILE 14

gap of 2.723613 A between ILE 14 and ASN 15

gap of 2.729245 A between ASN 15 and ALA 16

gap of 2.731725 A between ALA 16 and ILE 17

gap of 2.715459 A between ILE 17 and ILE 18

gap of 2.719024 A between ILE 18 and ARG 19

gap of 2.717810 A between ARG 19 and ALA 20

gap of 2.720303 A between ALA 20 and VAL 21

gap of 2.715599 A between VAL 21 and TYR 22

gap of 2.718147 A between TYR 22 and ARG 23

gap of 2.723344 A between ARG 23 and GLN 24

gap of 2.717319 A between GLN 24 and VAL 25

gap of 2.716876 A between VAL 25 and LEU 26

gap of 2.750609 A between LEU 26 and GLY 27

gap of 2.691271 A between GLY 27 and ASN 28

gap of 2.713609 A between ASN 28 and ASP 29

gap of 2.716595 A between ASP 29 and TYR 30

gap of 2.834376 A between TYR 30 and VAL 31

gap of 2.740735 A between VAL 31 and MET 32

gap of 2.762999 A between MET 32 and SER 33

gap of 2.779094 A between SER 33 and THR 34

gap of 2.774447 A between THR 34 and GLU 35

gap of 2.717173 A between GLU 35 and ARG 36

gap of 2.828097 A between ARG 36 and LEU 37

gap of 2.722025 A between LEU 37 and THR 38

gap of 2.726870 A between THR 38 and SER 39

gap of 2.717180 A between SER 39 and ALA 40

gap of 2.722091 A between ALA 40 and GLU 41

gap of 2.721927 A between GLU 41 and SER 42

gap of 2.728442 A between SER 42 and LEU 43

gap of 2.725169 A between LEU 43 and LEU 44

gap of 2.721238 A between LEU 44 and ARG 45

gap of 2.719078 A between ARG 45 and GLY 46

gap of 2.720800 A between GLY 46 and GLY 47

gap of 2.723865 A between GLY 47 and GLU 48

gap of 2.715152 A between GLU 48 and ILE 49

gap of 2.772826 A between ILE 49 and SER 50

gap of 2.761750 A between SER 50 and VAL 51

gap of 2.728095 A between VAL 51 and ARG 52

gap of 2.715574 A between ARG 52 and ASP 53

gap of 2.733038 A between ASP 53 and PHE 54

gap of 2.719329 A between PHE 54 and VAL 55

gap of 2.727999 A between VAL 55 and ARG 56

gap of 2.717188 A between ARG 56 and ALA 57

gap of 2.722254 A between ALA 57 and VAL 58

gap of 2.725930 A between VAL 58 and ALA 59

gap of 2.733883 A between ALA 59 and LEU 60

gap of 2.733427 A between LEU 60 and SER 61

gap of 2.713916 A between SER 61 and GLU 62

gap of 2.732963 A between GLU 62 and LEU 63

gap of 2.734959 A between LEU 63 and TYR 64

gap of 2.719423 A between TYR 64 and ARG 65

gap of 2.718073 A between ARG 65 and GLU 66

gap of 2.719209 A between GLU 66 and LYS 67

gap of 2.719891 A between LYS 67 and PHE 68

gap of 2.730991 A between PHE 68 and PHE 69

gap of 2.718244 A between PHE 69 and HIS 70

gap of 2.719154 A between HIS 70 and ASN 71

gap of 2.726478 A between ASN 71 and ASN 72

gap of 2.740933 A between ASN 72 and ALA 73

gap of 2.717431 A between ALA 73 and HIS 74

gap of 2.727621 A between HIS 74 and ASN 75

gap of 2.718141 A between ASN 75 and ARG 76

gap of 2.725775 A between ARG 76 and PHE 77

gap of 2.724600 A between PHE 77 and ILE 78

gap of 2.719225 A between ILE 78 and GLU 79

gap of 2.724940 A between GLU 79 and LEU 80

gap of 2.722557 A between LEU 80 and ASN 81

gap of 2.725496 A between ASN 81 and PHE 82

gap of 2.717104 A between PHE 82 and LYS 83

gap of 2.729854 A between LYS 83 and HIS 84

gap of 2.715890 A between HIS 84 and LEU 85

gap of 2.717792 A between LEU 85 and LEU 86

gap of 2.778396 A between LEU 86 and GLY 87

gap of 2.728306 A between GLY 87 and ARG 88

gap of 2.778821 A between ARG 88 and ALA 89

gap of 3.178963 A between ALA 89 and PRO 90

gap of 3.506716 A between PRO 90 and TYR 91

gap of 2.736086 A between TYR 91 and ASP 92

gap of 2.700804 A between ASP 92 and GLN 93

gap of 2.735856 A between GLN 93 and ALA 94

gap of 2.724033 A between ALA 94 and GLU 95

gap of 2.718034 A between GLU 95 and VAL 96

gap of 2.719740 A between VAL 96 and ALA 97

gap of 2.726361 A between ALA 97 and ALA 98

gap of 2.717269 A between ALA 98 and HIS 99

gap of 2.731185 A between HIS 99 and ALA 100

gap of 2.719558 A between ALA 100 and ALA 101

gap of 2.725414 A between ALA 101 and THR 102

gap of 2.719775 A between THR 102 and TYR 103

gap of 2.718216 A between TYR 103 and HIS 104

gap of 2.717378 A between HIS 104 and SER 105

gap of 2.718232 A between SER 105 and HIS 106

gap of 2.743360 A between HIS 106 and GLY 107

gap of 2.725111 A between GLY 107 and TYR 108

gap of 2.718243 A between TYR 108 and ASP 109

gap of 2.716697 A between ASP 109 and ALA 110

gap of 2.726271 A between ALA 110 and ASP 111

gap of 2.717010 A between ASP 111 and ILE 112

gap of 2.719857 A between ILE 112 and ASN 113

gap of 2.728598 A between ASN 113 and SER 114

gap of 2.724549 A between SER 114 and TYR 115

gap of 2.717839 A between TYR 115 and ILE 116

gap of 2.714807 A between ILE 116 and ASP 117

gap of 2.748667 A between ASP 117 and SER 118

gap of 2.726429 A between SER 118 and ALA 119

gap of 2.733695 A between ALA 119 and GLU 120

gap of 2.719500 A between GLU 120 and TYR 121

gap of 2.716120 A between TYR 121 and THR 122

gap of 2.811718 A between THR 122 and GLU 123

gap of 2.714656 A between GLU 123 and SER 124

gap of 2.716122 A between SER 124 and PHE 125

gap of 2.735861 A between PHE 125 and GLY 126

gap of 2.781337 A between GLY 126 and ASP 127

gap of 2.722933 A between ASP 127 and ASN 128

gap of 2.720974 A between ASN 128 and VAL 129

gap of 2.708716 A between VAL 129 and VAL 130

gap of 3.182773 A between VAL 130 and PRO 131

gap of 3.503148 A between PRO 131 and TYR 132

gap of 2.758885 A between TYR 132 and PHE 133

gap of 2.713678 A between PHE 133 and ARG 134

gap of 2.832077 A between ARG 134 and GLY 135

gap of 2.693330 A between GLY 135 and LEU 136

gap of 2.836470 A between LEU 136 and GLU 137

gap of 2.769203 A between GLU 137 and HIS 138

gap of 2.769918 A between HIS 138 and HIS 139

gap of 2.708929 A between HIS 139 and HIS 140

gap of 2.717320 A between HIS 140 and HIS 141

gap of 2.690360 A between HIS 141 and HIS 142

gap of 2.731565 A between HIS 142 and HIS 143

---------- Mising heavy atom(s)

None

Gordon Chalmers

Department of Computer Science

Complex Carbohydrate Research Center

University of Georgia

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Sat Nov 28 2020 - 20:00:02 PST

Date: Sun, 29 Nov 2020 03:43:05 +0000

I have a question about gaps that I will be solving

soon. Why does my Matlab protein structure software

produce this when using pdb4amber:

I am not new to amber, and the coordinates are good in

this file, which I made by rotating phi/psi/chi angles from

a linear structure. Nonplanar because I used dihedral

angles from the PDB model 1 structure to rotate about

the bonds from a linear structure, with amino acid coordinates

from the Cyana lib. There is no issue with PDB files, only

when I rotate angles and create a new pdb file which is in the

format, which I used pdb4format also to check the indentations.

I attached the initial linear peptide 2L3W 143 residue chain which

does not load correctly in pymol although the coordinates are

correct and can be seen. I am using the linear structure to find

the general one by rotating about dihedral bonds phi/psi and chi.

Simply rotating bonds should not cause problems in a pdb file if

done correctly, and certainly not produce gaps; I have checked

bond distances in my 'rotated' protein model. Attaching the

pdb files exceeds the Amber reflector memory limit.

(base) gordon.pop-os:~/Desktop/protein_program$ pdb4amber -i protein_2L3W_nonplanar.pdb -o protein_2L3W_nonplanar_nohyd.pdb --nohyd

==================================================

Summary of pdb4amber for: protein_2L3W_nonplanar.pdb

===================================================

----------Chains

The following (original) chains have been found:

A

---------- Alternate Locations (Original Residues!))

The following residues had alternate locations:

None

-----------Non-standard-resnames

---------- Gaps (Renumbered Residues!)

gap of 3.180778 A between MET 1 and PRO 2

gap of 3.532217 A between PRO 2 and LEU 3

gap of 2.706905 A between LEU 3 and GLU 4

gap of 2.701192 A between GLU 4 and TRP 5

gap of 2.716848 A between TRP 5 and ARG 6

gap of 2.755144 A between ARG 6 and ALA 7

gap of 2.804152 A between ALA 7 and GLY 8

gap of 2.709739 A between GLY 8 and ALA 9

gap of 2.704501 A between ALA 9 and SER 10

gap of 2.732872 A between SER 10 and SER 11

gap of 2.723781 A between SER 11 and ASP 12

gap of 2.719689 A between ASP 12 and GLU 13

gap of 2.720244 A between GLU 13 and ILE 14

gap of 2.723613 A between ILE 14 and ASN 15

gap of 2.729245 A between ASN 15 and ALA 16

gap of 2.731725 A between ALA 16 and ILE 17

gap of 2.715459 A between ILE 17 and ILE 18

gap of 2.719024 A between ILE 18 and ARG 19

gap of 2.717810 A between ARG 19 and ALA 20

gap of 2.720303 A between ALA 20 and VAL 21

gap of 2.715599 A between VAL 21 and TYR 22

gap of 2.718147 A between TYR 22 and ARG 23

gap of 2.723344 A between ARG 23 and GLN 24

gap of 2.717319 A between GLN 24 and VAL 25

gap of 2.716876 A between VAL 25 and LEU 26

gap of 2.750609 A between LEU 26 and GLY 27

gap of 2.691271 A between GLY 27 and ASN 28

gap of 2.713609 A between ASN 28 and ASP 29

gap of 2.716595 A between ASP 29 and TYR 30

gap of 2.834376 A between TYR 30 and VAL 31

gap of 2.740735 A between VAL 31 and MET 32

gap of 2.762999 A between MET 32 and SER 33

gap of 2.779094 A between SER 33 and THR 34

gap of 2.774447 A between THR 34 and GLU 35

gap of 2.717173 A between GLU 35 and ARG 36

gap of 2.828097 A between ARG 36 and LEU 37

gap of 2.722025 A between LEU 37 and THR 38

gap of 2.726870 A between THR 38 and SER 39

gap of 2.717180 A between SER 39 and ALA 40

gap of 2.722091 A between ALA 40 and GLU 41

gap of 2.721927 A between GLU 41 and SER 42

gap of 2.728442 A between SER 42 and LEU 43

gap of 2.725169 A between LEU 43 and LEU 44

gap of 2.721238 A between LEU 44 and ARG 45

gap of 2.719078 A between ARG 45 and GLY 46

gap of 2.720800 A between GLY 46 and GLY 47

gap of 2.723865 A between GLY 47 and GLU 48

gap of 2.715152 A between GLU 48 and ILE 49

gap of 2.772826 A between ILE 49 and SER 50

gap of 2.761750 A between SER 50 and VAL 51

gap of 2.728095 A between VAL 51 and ARG 52

gap of 2.715574 A between ARG 52 and ASP 53

gap of 2.733038 A between ASP 53 and PHE 54

gap of 2.719329 A between PHE 54 and VAL 55

gap of 2.727999 A between VAL 55 and ARG 56

gap of 2.717188 A between ARG 56 and ALA 57

gap of 2.722254 A between ALA 57 and VAL 58

gap of 2.725930 A between VAL 58 and ALA 59

gap of 2.733883 A between ALA 59 and LEU 60

gap of 2.733427 A between LEU 60 and SER 61

gap of 2.713916 A between SER 61 and GLU 62

gap of 2.732963 A between GLU 62 and LEU 63

gap of 2.734959 A between LEU 63 and TYR 64

gap of 2.719423 A between TYR 64 and ARG 65

gap of 2.718073 A between ARG 65 and GLU 66

gap of 2.719209 A between GLU 66 and LYS 67

gap of 2.719891 A between LYS 67 and PHE 68

gap of 2.730991 A between PHE 68 and PHE 69

gap of 2.718244 A between PHE 69 and HIS 70

gap of 2.719154 A between HIS 70 and ASN 71

gap of 2.726478 A between ASN 71 and ASN 72

gap of 2.740933 A between ASN 72 and ALA 73

gap of 2.717431 A between ALA 73 and HIS 74

gap of 2.727621 A between HIS 74 and ASN 75

gap of 2.718141 A between ASN 75 and ARG 76

gap of 2.725775 A between ARG 76 and PHE 77

gap of 2.724600 A between PHE 77 and ILE 78

gap of 2.719225 A between ILE 78 and GLU 79

gap of 2.724940 A between GLU 79 and LEU 80

gap of 2.722557 A between LEU 80 and ASN 81

gap of 2.725496 A between ASN 81 and PHE 82

gap of 2.717104 A between PHE 82 and LYS 83

gap of 2.729854 A between LYS 83 and HIS 84

gap of 2.715890 A between HIS 84 and LEU 85

gap of 2.717792 A between LEU 85 and LEU 86

gap of 2.778396 A between LEU 86 and GLY 87

gap of 2.728306 A between GLY 87 and ARG 88

gap of 2.778821 A between ARG 88 and ALA 89

gap of 3.178963 A between ALA 89 and PRO 90

gap of 3.506716 A between PRO 90 and TYR 91

gap of 2.736086 A between TYR 91 and ASP 92

gap of 2.700804 A between ASP 92 and GLN 93

gap of 2.735856 A between GLN 93 and ALA 94

gap of 2.724033 A between ALA 94 and GLU 95

gap of 2.718034 A between GLU 95 and VAL 96

gap of 2.719740 A between VAL 96 and ALA 97

gap of 2.726361 A between ALA 97 and ALA 98

gap of 2.717269 A between ALA 98 and HIS 99

gap of 2.731185 A between HIS 99 and ALA 100

gap of 2.719558 A between ALA 100 and ALA 101

gap of 2.725414 A between ALA 101 and THR 102

gap of 2.719775 A between THR 102 and TYR 103

gap of 2.718216 A between TYR 103 and HIS 104

gap of 2.717378 A between HIS 104 and SER 105

gap of 2.718232 A between SER 105 and HIS 106

gap of 2.743360 A between HIS 106 and GLY 107

gap of 2.725111 A between GLY 107 and TYR 108

gap of 2.718243 A between TYR 108 and ASP 109

gap of 2.716697 A between ASP 109 and ALA 110

gap of 2.726271 A between ALA 110 and ASP 111

gap of 2.717010 A between ASP 111 and ILE 112

gap of 2.719857 A between ILE 112 and ASN 113

gap of 2.728598 A between ASN 113 and SER 114

gap of 2.724549 A between SER 114 and TYR 115

gap of 2.717839 A between TYR 115 and ILE 116

gap of 2.714807 A between ILE 116 and ASP 117

gap of 2.748667 A between ASP 117 and SER 118

gap of 2.726429 A between SER 118 and ALA 119

gap of 2.733695 A between ALA 119 and GLU 120

gap of 2.719500 A between GLU 120 and TYR 121

gap of 2.716120 A between TYR 121 and THR 122

gap of 2.811718 A between THR 122 and GLU 123

gap of 2.714656 A between GLU 123 and SER 124

gap of 2.716122 A between SER 124 and PHE 125

gap of 2.735861 A between PHE 125 and GLY 126

gap of 2.781337 A between GLY 126 and ASP 127

gap of 2.722933 A between ASP 127 and ASN 128

gap of 2.720974 A between ASN 128 and VAL 129

gap of 2.708716 A between VAL 129 and VAL 130

gap of 3.182773 A between VAL 130 and PRO 131

gap of 3.503148 A between PRO 131 and TYR 132

gap of 2.758885 A between TYR 132 and PHE 133

gap of 2.713678 A between PHE 133 and ARG 134

gap of 2.832077 A between ARG 134 and GLY 135

gap of 2.693330 A between GLY 135 and LEU 136

gap of 2.836470 A between LEU 136 and GLU 137

gap of 2.769203 A between GLU 137 and HIS 138

gap of 2.769918 A between HIS 138 and HIS 139

gap of 2.708929 A between HIS 139 and HIS 140

gap of 2.717320 A between HIS 140 and HIS 141

gap of 2.690360 A between HIS 141 and HIS 142

gap of 2.731565 A between HIS 142 and HIS 143

---------- Mising heavy atom(s)

None

Gordon Chalmers

Department of Computer Science

Complex Carbohydrate Research Center

University of Georgia

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Sat Nov 28 2020 - 20:00:02 PST

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