[X-plor] how to create paramerter file for charmm simulations
saravana prakash
saravanprakash at yahoo.com
Tue Aug 15 10:53:24 EST 2006
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PSF
3 !NTITLE
REMARKS original generated structure x-plor psf file
REMARKS topology SARCOrigina153_autopsf-temp.top
REMARKS segment O1 { first NONE; last NONE; auto angles dihedrals }
36 !NATOM
1 O1 1 FRAG N1 NX -0.280000 14.0067 0
2 O1 1 FRAG C2 CT -0.063000 12.0110 0
3 O1 1 FRAG C3 CT -0.121000 12.0110 0
4 O1 1 FRAG C4 CT -0.010000 12.0110 0
5 O1 1 FRAG C5 CUA1 0.437000 12.0110 0
6 O1 1 FRAG C6 CUA1 0.230000 12.0110 0
7 O1 1 FRAG C7 CUA1 -0.298000 12.0110 0
8 O1 1 FRAG C8 C 0.437000 12.0110 0
9 O1 1 FRAG C9 CUA1 -0.207000 12.0110 0
10 O1 1 FRAG C10 CUA1 -0.285000 12.0110 0
11 O1 1 FRAG O11 OE -0.548000 15.9994 0
12 O1 1 FRAG C12 C 1.067000 12.0110 0
13 O1 1 FRAG C13 CUA1 -0.478000 12.0110 0
14 O1 1 FRAG C14 CUA1 -0.073000 12.0110 0
15 O1 1 FRAG C15 CT 0.089000 12.0110 0
16 O1 1 FRAG C16 CT 0.006000 12.0110 0
17 O1 1 FRAG C17 CT 0.019000 12.0110 0
18 O1 1 FRAG O18 O 0.620000 15.9994 0
19 O1 1 FRAG C19 CF3 1.357000 12.0110 0
20 O1 1 FRAG F20 XF -0.426000 18.9984 0
21 O1 1 FRAG F21 XF -0.431000 18.9984 0
22 O1 1 FRAG F22 XF -0.424000 18.9984 0
23 O1 1 FRAG H23 HA 0.089000 1.0080 0
24 O1 1 FRAG H24 HA 0.095000 1.0080 0
25 O1 1 FRAG H25 HA 0.070000 1.0080 0
26 O1 1 FRAG H26 HA 0.070000 1.0080 0
27 O1 1 FRAG H27 HA 0.041000 1.0080 0
28 O1 1 FRAG H28 HA 0.053000 1.0080 0
29 O1 1 FRAG H29 HA 0.233000 1.0080 0
30 O1 1 FRAG H30 HA 0.237000 1.0080 0
31 O1 1 FRAG H31 HA 0.028000 1.0080 0
32 O1 1 FRAG H32 HA 0.021000 1.0080 0
33 O1 1 FRAG H33 HA 0.011000 1.0080 0
34 O1 1 FRAG H34 HA 0.026000 1.0080 0
35 O1 1 FRAG H35 HA 0.064000 1.0080 0
36 O1 1 FRAG H36 HA 0.056000 1.0080 0
39 !NBOND: bonds
1 2 1 6 1 17 2 3
2 23 2 24 3 4 3 25
3 26 4 5 4 27 4 28
5 6 5 10 6 7 7 8
7 15 8 9 8 11 9 10
9 14 10 29 11 12 12 13
12 18 13 14 13 30 14 19
15 16 15 31 15 32 16 17
16 33 16 34 17 35 17 36
19 20 19 21 19 22
73 !NTHETA: angles
1 17 36 1 17 35 1 17 16
1 6 7 1 6 5 1 2 24
1 2 23 1 2 3 2 3 26
2 3 25 2 3 4 2 1 17
2 1 6 3 4 28 3 4 27
3 4 5 3 2 24 3 2 23
4 5 10 4 5 6 4 3 26
4 3 25 5 10 29 5 10 9
5 6 7 5 4 28 5 4 27
6 7 15 6 7 8 6 5 10
6 1 17 7 15 32 7 15 31
7 15 16 7 8 11 7 8 9
8 11 12 8 9 14 8 9 10
8 7 15 9 14 19 9 14 13
9 10 29 9 8 11 10 9 14
11 12 18 11 12 13 12 13 30
12 13 14 13 14 19 13 12 18
14 19 22 14 19 21 14 19 20
14 13 30 15 16 34 15 16 33
15 16 17 16 17 36 16 17 35
16 15 32 16 15 31 17 16 34
17 16 33 20 19 22 20 19 21
21 19 22 23 2 24 25 3 26
27 4 28 31 15 32 33 16 34
35 17 36
110 !NPHI: dihedrals
1 17 16 15 1 17 16 33
1 17 16 34 1 6 5 4
1 6 5 10 1 6 7 8
1 6 7 15 1 2 3 4
1 2 3 25 1 2 3 26
2 3 4 5 2 3 4 27
2 3 4 28 2 1 6 5
2 1 6 7 2 1 17 16
2 1 17 35 2 1 17 36
3 4 5 6 3 4 5 10
3 2 1 6 3 2 1 17
4 5 6 7 4 5 10 9
4 5 10 29 4 3 2 23
4 3 2 24 5 10 9 8
5 10 9 14 5 6 1 17
5 6 7 8 5 6 7 15
5 4 3 25 5 4 3 26
6 7 8 9 6 7 8 11
6 7 15 16 6 7 15 31
6 7 15 32 6 5 4 27
6 5 4 28 6 5 10 9
6 5 10 29 6 1 2 23
6 1 2 24 6 1 17 16
6 1 17 35 6 1 17 36
7 15 16 17 7 15 16 33
7 15 16 34 7 8 9 10
7 8 9 14 7 8 11 12
7 6 1 17 7 6 5 10
8 11 12 13 8 11 12 18
8 9 10 29 8 9 14 13
8 9 14 19 8 7 15 16
8 7 15 31 8 7 15 32
9 14 13 12 9 14 13 30
9 14 19 20 9 14 19 21
9 14 19 22 9 8 7 15
9 8 11 12 10 9 8 11
10 9 14 13 10 9 14 19
10 5 4 27 10 5 4 28
11 12 13 14 11 12 13 30
11 8 7 15 11 8 9 14
12 13 14 19 13 14 19 20
13 14 19 21 13 14 19 22
14 13 12 18 14 9 10 29
15 16 17 35 15 16 17 36
17 16 15 31 17 16 15 32
17 1 2 23 17 1 2 24
18 12 13 30 19 14 13 30
23 2 3 25 23 2 3 26
24 2 3 25 24 2 3 26
25 3 4 27 25 3 4 28
26 3 4 27 26 3 4 28
31 15 16 33 31 15 16 34
32 15 16 33 32 15 16 34
33 16 17 35 33 16 17 36
34 16 17 35 34 16 17 36
0 !NIMPHI: impropers
0 !NDON: donors
0 !NACC: acceptors
0 !NNB
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0
1 0 !NGRP
0 0 0
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* ...
* Insight II generated topology file for SARCORIGINA153
* Produced on Mon Aug 14 23:39:14 2006
*
22 0
MASS 33 NX 14.00670 N
MASS 10 CT 12.01100 C
MASS 16 CUA1 12.01100 C
MASS 14 C 12.01100 C
MASS 50 OE 15.99940 O
MASS 40 O 15.99940 O
MASS 232 CF3 12.01100 C
MASS 92 XF 18.99840 F
MASS 3 HA 1.00800 H
AUTO ANGLES DIHE
DEFAULT FIRST NONE LAST NONE
RESI FRAG 0.001
GROUP
ATOM N1 NX -0.280
ATOM C2 CT -0.063
ATOM C3 CT -0.121
ATOM C4 CT -0.010
ATOM C5 CUA1 0.437
ATOM C6 CUA1 0.230
ATOM C7 CUA1 -0.298
ATOM C8 C 0.437
ATOM C9 CUA1 -0.207
ATOM C10 CUA1 -0.285
ATOM O11 OE -0.548
ATOM C12 C 1.067
ATOM C13 CUA1 -0.478
ATOM C14 CUA1 -0.073
ATOM C15 CT 0.089
ATOM C16 CT 0.006
ATOM C17 CT 0.019
ATOM O18 O 0.620
ATOM C19 CF3 1.357
ATOM F20 XF -0.426
ATOM F21 XF -0.431
ATOM F22 XF -0.424
ATOM H23 HA 0.089
ATOM H24 HA 0.095
ATOM H25 HA 0.070
ATOM H26 HA 0.070
ATOM H27 HA 0.041
ATOM H28 HA 0.053
ATOM H29 HA 0.233
ATOM H30 HA 0.237
ATOM H31 HA 0.028
ATOM H32 HA 0.021
ATOM H33 HA 0.011
ATOM H34 HA 0.026
ATOM H35 HA 0.064
ATOM H36 HA 0.056
BOND N1 C2 N1 C6 N1 C17 C2 C3 C2 H23
BOND C2 H24 C3 C4 C3 H25 C3 H26 C4 C5
BOND C4 H27 C4 H28 C5 C6 C5 C10 C6 C7
BOND C7 C8 C7 C15 C8 C9 C8 O11 C9 C10
BOND C9 C14 C10 H29 O11 C12 C12 C13 C12 O18
BOND C13 C14 C13 H30 C14 C19 C15 C16 C15 H31
BOND C15 H32 C16 C17 C16 H33 C16 H34 C17 H35
BOND C17 H36 C19 F20 C19 F21 C19 F22
ACCEPTOR O11 C8
ACCEPTOR O11 C12
ACCEPTOR O18 C12
IC C6 N1 C2 C3 1.3920 119.3801 49.2724 108.2697 1.5375
IC C6 N1 C2 H23 1.3920 119.3801 166.2319 110.8846 1.0952
IC C6 N1 C2 H24 1.3920 119.3801 -74.2566 109.9224 1.0865
IC C17 N1 C2 C3 1.4692 115.6335 -149.9597 108.2697 1.5375
IC C2 N1 C6 C5 1.4806 119.3801 -20.7341 119.5837 1.3867
IC C2 N1 C6 C7 1.4806 119.3801 158.9072 120.8169 1.3924
IC C2 N1 C17 C16 1.4806 115.6335 174.5031 112.7254 1.5245
IC C2 N1 C17 H35 1.4806 115.6335 54.5190 108.8323 1.0995
IC C2 N1 C17 H36 1.4806 115.6335 -62.2515 108.9695 1.0954
IC N1 C2 C3 C4 1.4806 108.2697 -57.1079 111.0457 1.5187
IC N1 C2 C3 H25 1.4806 108.2697 64.1335 108.0549 1.0960
IC N1 C2 C3 H26 1.4806 108.2697 -178.9383 108.7188 1.0940
IC C2 C3 C4 C5 1.5375 111.0457 39.2389 113.5468 1.5161
IC C2 C3 C4 H27 1.5375 111.0457 -80.9928 110.1638 1.0985
IC C2 C3 C4 H28 1.5375 111.0457 160.5459 110.3298 1.0961
IC C3 C4 C5 C6 1.5187 113.5468 -10.4537 122.1896 1.3867
IC C3 C4 C5 C10 1.5187 113.5468 169.7630 117.5892 1.4086
IC N1 C6 C5 C4 1.3920 119.5837 -0.2547 122.1896 1.5161
IC C4 C5 C10 C9 1.5161 117.5892 179.7260 121.0217 1.3839
IC C4 C5 C10 H29 1.5161 117.5892 -0.1511 115.8608 1.0763
IC N1 C6 C7 C8 1.3920 120.8169 -179.2604 119.4399 1.4007
IC N1 C6 C7 C15 1.3920 120.8169 0.3172 120.9138 1.5056
IC C6 C7 C8 C9 1.3924 119.4399 -0.4707 121.7214 1.3971
IC C6 C7 C8 O11 1.3924 119.4399 179.1014 118.5808 1.3575
IC C6 C7 C15 C16 1.3924 120.9138 25.3954 111.8223 1.5375
IC C6 C7 C15 H31 1.3924 120.9138 -96.8956 109.3651 1.0942
IC C6 C7 C15 H32 1.3924 120.9138 144.0121 112.0035 1.0968
IC C7 C8 C9 C10 1.4007 121.7214 0.2849 117.9962 1.3839
IC C7 C8 C9 C14 1.4007 121.7214 -179.8160 119.8282 1.4578
IC C7 C8 O11 C12 1.4007 118.5808 -179.1605 122.5352 1.3448
IC C5 C10 C9 C8 1.4086 121.0217 -0.0174 117.9962 1.3971
IC C8 C9 C14 C13 1.3971 119.8282 -0.8183 118.0830 1.3507
IC C8 C9 C14 C19 1.3971 119.8282 179.0570 123.3163 1.4989
IC C8 O11 C12 C13 1.3575 122.5352 -1.2053 119.3336 1.4514
IC C8 O11 C12 O18 1.3575 122.5352 178.8801 119.4809 1.2214
IC O11 C12 C13 C14 1.3448 119.3336 0.9578 120.5103 1.3507
IC O11 C12 C13 H30 1.3448 119.3336 -178.9461 116.6919 1.0799
IC C9 C14 C13 C12 1.4578 118.0830 0.0412 120.5103 1.4514
IC C9 C14 C19 F20 1.4578 123.3163 -58.0808 109.0871 1.3952
IC C9 C14 C19 F21 1.4578 123.3163 -179.1178 117.8324 1.3694
IC C9 C14 C19 F22 1.4578 123.3163 59.7627 108.8958 1.3945
IC C7 C15 C16 C17 1.5056 111.8223 -49.1523 110.5925 1.5245
IC C7 C15 C16 H33 1.5056 111.8223 -168.6718 108.3476 1.0952
IC C7 C15 C16 H34 1.5056 111.8223 72.9659 110.4359 1.0925
IC N1 C17 C16 C15 1.4692 112.7254 49.3367 110.5925 1.5375
PRES DISU -0.20
! This patch is used to provide a disulphide bridge between two CYS residues
GROUP
ATOM 1CB CT -0.10
ATOM 1SG ST -0.00
GROUP
ATOM 2SG ST -0.00
ATOM 2CB CT -0.10
DELETE ATOM 1HG
DELETE ATOM 2HG
BOND 1SG 2SG
ANGLE 1CB 1SG 2SG 1SG 2SG 2CB
DIHE 1CA 1CB 1SG 2SG 1HB1 1CB 1SG 2SG 1HB2 1CB 1SG 2SG
DIHE 1CB 1SG 2SG 2CB
DIHE 1SG 2SG 2CB 2CA 1SG 2SG 2CB 2HB1 1SG 2SG 2CB 2HB2
IC 1CA 1CB 1SG 2SG 0.0 0.0 180.0 0.0 0.0
IC 1CB 1SG 2SG 2CB 0.0 0.0 180.0 0.0 0.0
IC 1SG 2SG 2CB 2CA 0.0 0.0 180.0 0.0 0.0
END
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