Abhinav Kumar writes:
> Hi
>
> How can I change torsional angles in a RNA model? The O data file "torsion.o"
> doesn't seem to contain any RNA related stuff.
>
> Any help is appreciated.
>
Here's a useful torsion dictionary, edit as required
1) amino-acids are defined as sidechains torsions only (more useful)
2) RNA/DNA you may have to rename atoms & residues depending on your
naming conventions (is adenine A or ADE etc?)
3) some other things
Phil
torsion_information t 239 72
RESIDUE ALA
RESIDUE ARG
TORSION CHI1 -60. N CA CB CG CG CD NE CZ NH1 NH2
TORSION CHI2 180. CA CB CG CD CD NE CZ NH1 NH2
TORSION CHI3 180. CB CG CD NE NE CZ NH1 NH2
TORSION CHI4 180. CG CD NE CZ CZ NH1 NH2
RESIDUE CYS
TORSION CHI1 -60. N CA CB SG SG
RESIDUE CYH
TORSION CHI1 -60. N CA CB SG SG
RESIDUE ASN
TORSION CHI1 -60. N CA CB CG CG OD1 ND2
TORSION CHI2 0. CA CB CG OD1 OD1 ND2
RESIDUE ASP
TORSION CHI1 -60. N CA CB CG CG OD1 OD2
TORSION CHI2 0. CA CB CG OD1 OD1 OD2
RESIDUE GLU
TORSION CHI1 -60. N CA CB CG CG CD OE1 OE2
TORSION CHI2 180. CA CB CG CD CD OE1 OE2
TORSION CHI3 0. CB CG CD OE1 OE1 OE2
RESIDUE GLN
TORSION CHI1 -60. N CA CB CG CG CD OE1 NE2
TORSION CHI2 180. CA CB CG CD CD OE1 NE2
TORSION CHI3 0. CB CG CD OE1 OE1 NE2
RESIDUE GLY
RESIDUE HIS
TORSION CHI1 -60. N CA CB CG CG ND1 CD2 CE1 NE2
TORSION CHI2 -60. CA CB CG ND1 ND1 CD2 CE1 NE2
RESIDUE ILE
TORSION CHI1 -60. N CA CB CG1 CG1 CD1 CG2
TORSION CHI2 180. CA CB CG1 CD1 CD1
RESIDUE LEU
TORSION CHI1 -60. N CA CB CG CG CD1 CD2
TORSION CHI2 180. CA CB CG CD1 CD1 CD2
RESIDUE LYS
TORSION CHI1 -60. N CA CB CG CG CD CE NZ
TORSION CHI2 180. CA CB CG CD CD CE NZ
TORSION CHI3 180. CB CG CD CE CE NZ
TORSION CHI4 180. CG CD CE NZ NZ
RESIDUE MET
TORSION CHI1 -60. N CA CB CG CG SD CE
TORSION CHI2 -60. CA CB CG SD SD CE
TORSION CHI3 -60. CB CG SD CE CE
RESIDUE PHE
TORSION CHI1 -60. N CA CB CG CG CD1 CD2 CE1 CE2 CZ
TORSION CHI2 -90. CA CB CG CD1 CD1 CD2 CE1 CE2 CZ
RESIDUE PRO
RESIDUE SER
TORSION CHI1 -60. N CA CB OG OG
RESIDUE THR
TORSION CHI1 -60. N CA CB OG1 OG1 CG2
RESIDUE TYR
TORSION CHI1 -60. N CA CB CG CG CD1 CD2 CE1 CE2 CZ OH
TORSION CHI2 -90. CA CB CG CD1 CD1 CD2 CE1 CE2 CZ OH
RESIDUE TRP
TORSION CHI1 -60. N CA CB CG CG CD1 CD2 NE1 CE2 CE3 CZ2 CZ3 CH2
TORSION CHI2 -90. CA CB CG CD1 CD1 CD2 NE1 CE2 CE3 CZ2 CZ3 CH2
RESIDUE VAL
TORSION CHI1 60. N CA CB CG1 CG1 CG2
RESIDUE A
TORSION ALP 180 O4' C1' N9 C8 C8 C4 C5 N7 N3 C2 N1 C6 N6
TORSION BET 180 C8 N9 C1' O4' O4' C4' C3' O3' C2' O2' C5' O5' P \
O1P O2P
TORSION GAM 180 O4' C4' C5' O5' O5' P O1P O2P
TORSION DEL 180 C4' C5' O5' P P O1P O2P
TORSION EPS 180 C5' O5' P O1P O1P O2P
TORSION KAP 180 O5' C5' C4' C3' C3' O3' C2' O2' C1' O4' N9 C8 \
C4 C5 N7 N3 C2 N1 C6 N6
RESIDUE G
TORSION ALP 180 O4' C1' N9 C8 C8 C4 C5 N7 N3 C2 N1 C6 O6 N2
TORSION BET 180 C8 N9 C1' O4' O4' C4' C3' O3' C2' O2' C5' O5' P \
O1P O2P
TORSION GAM 180 O4' C4' C5' O5' O5' P O1P O2P
TORSION DEL 180 C4' C5' O5' P P O1P O2P
TORSION EPS 180 C5' O5' P O1P O1P O2P
TORSION KAP 180 O5' C5' C4' C3' C3' O3' C2' O2' C1' O4' N9 C8 \
C4 C5 N7 N3 C2 N1 C6 O6 N2
RESIDUE C
TORSION ALP 180 C2' C1' N1 C6 C5 C4 N4 N3 C2 O2 C6
TORSION BET 180 C6 N1 C1' O4' O4' C2' O2' C3' O3' C4' C5' O5' \
P O1P O2P
TORSION GAM 180 O4' C4' C5' O5' O5' P O1P O2P
TORSION DEL 180 C4' C5' O5' P P O1P O2P
TORSION EPS 180 C5' O5' P O1P O1P O2P
TORSION KAP 180 O5' C5' C4' C3' C3' O3' C2' O2' C1' O4' N1 C6 \
C5 C4 N4 N3 C2 O2
RESIDUE U
TORSION ALP 180 C2' C1' N1 C6 C5 C4 O4 N3 C2 O2 C6
TORSION BET 180 C6 N1 C1' O4' O4' C2' O2' C3' O3' C4' C5' O5' \
P O1P O2P
TORSION GAM 180 O4' C4' C5' O5' O5' P O1P O2P
TORSION DEL 180 C4' C5' O5' P P O1P O2P
TORSION EPS 180 C5' O5' P O1P O1P O2P
TORSION KAP 180 O5' C5' C4' C3' C3' O3' C2' O2' C1' O4' N1 C6 \
C5 C4 O4 N3 C2 O2
RESIDUE T
TORSION ALPH -46 O3'- P O5' C5' C5' C4' O4' C1' C2' C3' O3' N1 C2 N3 \
C4 C5 C6 O2 O4 C5A
TORSION BETA -146 P O5' C5' C4' C4' O4' C1' C2' C3' O3' N1 C2 N3 \
C4 C5 C6 O2 O4 C5A
TORSION GAMM 36 O5' C5' C4' C3' O4' C1' C2' C3' O3' N1 C2 N3 \
C4 C5 C6 O2 O4 C5A
TORSION DELT 156 C5' C4' C3' O3' O4' C1' C2' O3' N1 C2 N3 \
C4 C5 C6 O2 O4 C5A
TORSION EPSI 155 C4' C3' O3' P+
TORSION ZETA -96 C3' O3' P+ O5'+
TORSION CHI -98 O4' C1' N1 C2 N1 C2 N3 \
C4 C5 C6 O2 O4 C5A
RESIDUE ADE
TORSION ALP 180 O4' C1' N9 C8 C8 C4 C5 N7 N3 C2 N1 C6 N6
TORSION BET 180 C8 N9 C1' O4' O4' C4' C3' O3' C2' O2' C5' O5' P \
O1P O2P
TORSION GAM 180 O4' C4' C5' O5' O5' P O1P O2P
TORSION DEL 180 C4' C5' O5' P P O1P O2P
TORSION EPS 180 C5' O5' P O1P O1P O2P
TORSION KAP 180 O5' C5' C4' C3' C3' O3' C2' O2' C1' O4' N9 C8 \
C4 C5 N7 N3 C2 N1 C6 N6
RESIDUE GUA
TORSION ALP 180 O4' C1' N9 C8 C8 C4 C5 N7 N3 C2 N1 C6 O6 N2
TORSION BET 180 C8 N9 C1' O4' O4' C4' C3' O3' C2' O2' C5' O5' P \
O1P O2P
TORSION GAM 180 O4' C4' C5' O5' O5' P O1P O2P
TORSION DEL 180 C4' C5' O5' P P O1P O2P
TORSION EPS 180 C5' O5' P O1P O1P O2P
TORSION KAP 180 O5' C5' C4' C3' C3' O3' C2' O2' C1' O4' N9 C8 \
C4 C5 N7 N3 C2 N1 C6 O6 N2
RESIDUE CYT
TORSION ALP 180 C2' C1' N1 C6 C5 C4 N4 N3 C2 O2 C6
TORSION BET 180 C6 N1 C1' O4' O4' C2' O2' C3' O3' C4' C5' O5' \
P O1P O2P
TORSION GAM 180 O4' C4' C5' O5' O5' P O1P O2P
TORSION DEL 180 C4' C5' O5' P P O1P O2P
TORSION EPS 180 C5' O5' P O1P O1P O2P
TORSION KAP 180 O5' C5' C4' C3' C3' O3' C2' O2' C1' O4' N1 C6 \
C5 C4 N4 N3 C2 O2
RESIDUE URA
TORSION ALP 180 C2' C1' N1 C6 C5 C4 O4 N3 C2 O2 C6
TORSION BET 180 C6 N1 C1' O4' O4' C2' O2' C3' O3' C4' C5' O5' \
P O1P O2P
TORSION GAM 180 O4' C4' C5' O5' O5' P O1P O2P
TORSION DEL 180 C4' C5' O5' P P O1P O2P
TORSION EPS 180 C5' O5' P O1P O1P O2P
TORSION KAP 180 O5' C5' C4' C3' C3' O3' C2' O2' C1' O4' N1 C6 \
C5 C4 O4 N3 C2 O2
RESIDUE THY
TORSION ALP 180 C2' C1' N1 C2 N3 C4 C5 C6 O2 O4 C5A
TORSION BET 180 C6 N1 C1' O4' O4' C2' O2' C3' O3' C4' C5' O5' \
P O1P O2P
TORSION GAM 180 O4' C4' C5' O5' O5' P O1P O2P
TORSION DEL 180 C4' C5' O5' P P O1P O2P
TORSION EPS 180 C5' O5' P O1P O1P O2P
TORSION KAP 180 O5' C5' C4' C3' C3' O3' C2' O2' C1' O4' \
N1 C2 N3 C4 C5 C6 O2 O4 C5A
RESIDUE ATP
TORSION CHI -140. O4' C1' N9 C4 N1 C2 N3 C4 C5 C6 N6 N7 C8
TORSION GAMMA 180. C3' C4' C5' O5' O5' P1 O11 O12 O6 P2 O21 O22 O7 P3 \
O31 O32 O8
TORSION BETA 180. C4' C5' O5' P1 P1 O11 O12 O6 P2 O21 O22 O7 P3 O31 O32 O8
TORSION ALPHA 180. C5' O5' P1 O6 O11 O12 O6 P2 O21 O22 O7 P3 O31 O32 O8
TORSION TAU1 180. O5' P1 O6 P2 P2 O21 O22 O7 P3 O31 O32 O8
TORSION TAU2 180. P1 O6 P2 O7 O21 O22 O7 P3 O31 O32 O8
TORSION TAU3 180. O6 P2 O7 P3 P3 O31 O32 O8
TORSION TAU4 180. P2 O7 P3 O8 O31 O32 O8
RESIDUE ADP
TORSION CHI -140. O4' C1' N9 C4 N1 C2 N3 C4 C5 C6 N6 N7 C8
TORSION GAMMA 180. C3' C4' C5' O5' O5' P1 O11 O12 O6 P2 O21 O22 O7
TORSION BETA 180. C4' C5' O5' P1 P1 O11 O12 O6 P2 O21 O22 O7
TORSION ALPHA 180. C5' O5' P1 O6 O11 O12 O6 P2 O21 O22 O7
TORSION TAU1 180. O5' P1 O6 P2 P2 O21 O22 O7
TORSION TAU2 180. P1 O6 P2 O7 O21 O22 O7
RESIDUE COA
TORSION CHI -140. O4' C1' N9 C4 N1 C2 N3 C4 C5 C6 N6 N7 C8
TORSION PHI' 180. C2' C3' O3' P3 P3 O31 O32 O33
TORSION OMEGA' 180. C3' O3' P3 O31 O31 O32 O33
TORSION PSI 180. C3' C4' C5' O5' \
O5' P1 O11 O12 O6 P2 O21 O22 O7 CPB CPA CP8 CP9 CP7 OP3 \
CP6 OP2 NP2 CP5 CP4 CP3 OP1 NP1 CP2 CP1 S
TORSION PHI 180. C4' C5' O5' P1 \
P1 O11 O12 O6 P2 O21 O22 O7 CPB CPA CP8 CP9 CP7 OP3 \
CP6 OP2 NP2 CP5 CP4 CP3 OP1 NP1 CP2 CP1 S
TORSION OMEGA 180. C5' O5' P1 O6 \
O6 O11 O12 O6 P2 O21 O22 O7 CPB CPA CP8 CP9 CP7 OP3 \
CP6 OP2 NP2 CP5 CP4 CP3 OP1 NP1 CP2 CP1 S
TORSION TAU1 180. O5' P1 O6 P2 \
P2 O21 O22 O7 CPB CPA CP8 CP9 CP7 OP3 \
CP6 OP2 NP2 CP5 CP4 CP3 OP1 NP1 CP2 CP1 S
TORSION TAU2 180. P1 O6 P2 O7 \
O7 CPB CPA CP8 CP9 CP7 OP3 \
CP6 OP2 NP2 CP5 CP4 CP3 OP1 NP1 CP2 CP1 S
TORSION TAU3 180. O6 P2 O7 CPB \
CPB CPA CP8 CP9 CP7 OP3 \
CP6 OP2 NP2 CP5 CP4 CP3 OP1 NP1 CP2 CP1 S
TORSION TAU4 180. P2 O7 CPB CPA \
CPA CP8 CP9 CP7 OP3 \
CP6 OP2 NP2 CP5 CP4 CP3 OP1 NP1 CP2 CP1 S
TORSION TAU5 180. O7 CPB CPA CP7 \
CP7 OP3 \
CP6 OP2 NP2 CP5 CP4 CP3 OP1 NP1 CP2 CP1 S
TORSION TAU6 180. CPB CPA CP7 CP6 \
CP6 OP2 NP2 CP5 CP4 CP3 OP1 NP1 CP2 CP1 S
TORSION TAU7 180. CPA CP7 CP6 NP2 \
NP2 CP5 CP4 CP3 OP1 NP1 CP2 CP1 S
TORSION TAU8 180. CP7 CP6 NP2 CP5 \
CP5 CP4 CP3 OP1 NP1 CP2 CP1 S
TORSION TAU9 180. CP6 NP2 CP5 CP4 CP4 CP3 OP1 NP1 CP2 CP1 S
TORSION TAU10 180. NP2 CP5 CP4 CP3 CP3 OP1 NP1 CP2 CP1 S
TORSION TAU11 180. CP5 CP4 CP3 NP1 NP1 CP2 CP1 S
TORSION TAU12 180. CP4 CP3 NP1 CP2 CP2 CP1 S
TORSION TAU13 180. CP3 NP1 CP2 CP1 CP1 S
TORSION TAU14 180. NP1 CP2 CP1 S S
RESIDUE B12
!TORSION TAU11 180. C1 C2 C26 C27 C27 O28 N29
!TORSION TAU12 180. C2 C26 C27 O28 O28 N29
!TORSION TAU21 180. C2 C3 C30 C31 C31 C32 O34 N33
!TORSION TAU22 180. C3 C30 C31 C32 C32 O34 N33
!TORSION TAU23 180. C30 C31 C32 O34 O34 N33
TORSION TAU31 180. C6 C7 C37 C38 C38 O39 N40
TORSION TAU32 180. C7 C37 C38 O39 O39 N40
TORSION TAU41 180. C7 C8 C41 C42 C42 C43 O44 N45
TORSION TAU42 180. C8 C41 C42 C43 C43 O44 N45
TORSION TAU43 180. C41 C42 C43 O44 O44 N45
TORSION TAU51 180. C12 C13 C48 C49 C49 C50 O51 N52
TORSION TAU52 180. C13 C48 C49 C50 C50 O51 N52
TORSION TAU53 180. C48 C49 C50 O51 O51 N52
TORSION TAU61 180. C17 C18 C60 C61 C61 O63 N62
TORSION TAU62 180. C18 C60 C61 O63 O63 N62
RESIDUE MCD
TORSION TAU1 180. CP4 NP1 CP2 CP1 CP1 CPS CS1 OS1 CS2 CS3 CS4 OS4 OS5
TORSION TAU2 180. NP1 CP2 CP1 CPS CPS CS1 OS1 CS2 CS3 CS4 OS4 OS5
TORSION TAU3 180. CP2 CP1 CPS CS1 CS1 OS1 CS2 CS3 CS4 OS4 OS5
TORSION TAU4 180. CP1 CPS CS1 CS2 OS1 CS2 CS3 CS4 OS4 OS5
TORSION TAU5 180. CPS CS1 CS2 CS4 CS3 CS4 OS4 OS5
TORSION TAU6 180. CS1 CS2 CS4 OS4 OS4 OS5
RESIDUE ADD
TORSION CHI 180. C4 N9 C1' C2' C2' O2' C3' O3' C4' O4' C5'
TORSION CHIB 180. C2' C1' N9 C8 C8 C4 C5 N7 N3 C2 N1 C6 N6
RESIDUE GOL
TORSION TAU1 180. C3 C2 C1 O1 O1
TORSION TAU2 180. C1 C2 C3 O3 O3
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