[gmx-users] Self made GDP topology file.......deforms severely with LINC warning during EM and stopped
Zhenting Gao
zhentg at 163.com
Thu Nov 4 19:06:44 CET 2004
Hi gmx-users,
A GDP is in my protein complex. So I made my own Gromos 96 FF topology file for GDP.
First, I get the topology from PRODRG server.
Then I use Gaussian to recalculate the atom charge.
At last I refer to the topology of ATP and GUA in ffG43a1.rtp to modify the topology file for GDP.
However, the GDP deforms severely during the EM, and even crashes if I run a heating process.(it deforms whether I add positive ion or not. )
In contrast, the topology files generated by pdb2gmx for ATP and DGUA make the structure ramain good during a 300K heating process.
Why it deforms? It is the wrong force parameter? Or the wrong atom charge?
Please help me to check. The topology files are listed as below.
Thanks.
GDP.gro
-------------------------------------------------------------------------------
PRODRG COORDS
33
1GDP O2B 1 13.796 -0.791 5.821
1GDP PB 2 13.911 -0.692 5.803
1GDP O3B 3 14.047 -0.756 5.808
1GDP O1B 4 13.899 -0.581 5.703
1GDP O3A 5 13.903 -0.603 5.936
1GDP PA 6 13.884 -0.674 6.079
1GDP O1A 7 13.832 -0.817 6.074
1GDP O2A 8 14.009 -0.643 6.156
1GDP O5' 9 13.765 -0.580 6.127
1GDP C5' 10 13.801 -0.458 6.192
1GDP C4' 11 13.672 -0.403 6.247
1GDP O4' 12 13.568 -0.441 6.158
1GDP C3' 13 13.636 -0.465 6.382
1GDP O3' 14 13.660 -0.381 6.493
1GDP HAA 15 13.759 -0.370 6.506
1GDP C2' 16 13.487 -0.474 6.373
1GDP O2' 17 13.439 -0.353 6.433
1GDP HAB 18 13.339 -0.352 6.431
1GDP C1' 19 13.448 -0.469 6.227
1GDP N9 20 13.387 -0.597 6.187
1GDP C8 21 13.442 -0.705 6.127
1GDP N7 22 13.347 -0.801 6.108
1GDP C5 23 13.232 -0.754 6.159
1GDP C4 24 13.259 -0.620 6.214
1GDP N3 25 13.162 -0.549 6.273
1GDP C2 26 13.036 -0.595 6.285
1GDP N2 27 12.943 -0.515 6.342
1GDP HAE 28 12.968 -0.423 6.373
1GDP HAD 29 12.848 -0.547 6.352
1GDP N1 30 13.002 -0.717 6.239
1GDP HAC 31 12.907 -0.748 6.248
1GDP C6 32 13.093 -0.798 6.183
1GDP O6 33 13.058 -0.909 6.144
-------------------------------------------------------------------------------
GDP.top
-------------------------------------------------------------------------------
; This file is modified to Gromos 96 FF on 20041104
;
; This file was generated by PRODRG version 041015.0515
; PRODRG written/copyrighted by Daan van Aalten
;
; Questions/comments to dava at davapc1.bioch.dundee.ac.uk
;
; When using this software in a publication, cite:
; A. W. Schuettelkopf and D. M. F. van Aalten (2004).
; PRODRG - a tool for high-throughput crystallography
; of protein-ligand complexes.
; Acta Crystallogr. D60, 1355--1363.
; Include forcefield parameters
#include "ffG43a1.itp"
[ moleculetype ]
; Name nrexcl
GDP 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 OM 1 GDP O2B 1 -0.941 15.9994
2 P 1 GDP PB 1 1.334 30.9738
3 OM 1 GDP O3B 1 -0.975 15.9994
4 OM 1 GDP O1B 1 -1.043 15.9994
5 OA 1 GDP O3A 2 -0.482 15.9994
6 P 1 GDP PA 2 1.429 30.9738
7 OM 1 GDP O1A 2 -0.852 15.9994
8 OM 1 GDP O2A 2 -0.949 15.9994
9 OA 1 GDP O5' 2 -0.672 15.9994
10 CH2 1 GDP C5' 3 0.179 14.0270
11 CH1 1 GDP C4' 3 0.362 13.0190
12 OA 1 GDP O4' 3 -0.412 15.9994
13 CH1 1 GDP C3' 4 0.233 13.0190
14 OA 1 GDP O3' 4 -0.710 15.9994
15 H 1 GDP HAA 4 0.399 1.0080
16 CH1 1 GDP C2' 5 0.419 13.0190
17 OA 1 GDP O2' 5 -0.686 15.9994
18 H 1 GDP HAB 5 0.357 1.0080
19 CH1 1 GDP C1' 5 0.140 13.0190
20 NR 1 GDP N9 6 0.113 14.0067
21 CR1 1 GDP C8 6 0.354 13.0190
22 NR 1 GDP N7 7 -0.497 14.0067
23 C 1 GDP C5 7 -0.025 12.0110
24 C 1 GDP C4 7 0.245 12.0110
25 NR 1 GDP N3 7 -0.822 14.0067
26 C 1 GDP C2 7 1.075 12.0110
27 NT 1 GDP N2 8 -1.184 14.0067
28 H 1 GDP HAE 8 0.475 1.0080
29 H 1 GDP HAD 8 0.454 1.0080
30 NR 1 GDP N1 9 -0.791 14.0067
31 H 1 GDP HAC 9 0.403 1.0080
32 C 1 GDP C6 9 0.749 12.0110
33 O 1 GDP O6 9 -0.679 15.9994
[ bonds ]
; ai aj fu c0, c1, ...
1 2 2 gb_23 ;0.161 251040.0 0.161 251040.0 ; O2B PB
2 3 2 gb_23 ;0.161 251040.0 0.161 251040.0 ; PB O3B
2 4 2 gb_23 ;0.148 376560.0 0.148 376560.0 ; PB O1B
2 5 2 gb_27 ;0.161 251040.0 0.161 251040.0 ; PB O3A
5 6 2 gb_27 ;0.161 251040.0 0.161 251040.0 ; O3A PA
6 7 2 gb_23 ;0.148 376560.0 0.148 376560.0 ; PA O1A
6 8 2 gb_23 ;0.148 376560.0 0.148 376560.0 ; PA O2A
6 9 2 gb_27 ;0.161 251040.0 0.161 251040.0 ; PA O5'
9 10 2 gb_19 ;0.143 251040.0 0.143 251040.0 ; O5' C5'
10 11 2 gb_25 ;0.153 251040.0 0.153 251040.0 ; C5' C4'
11 12 2 gb_19 ;0.144 251040.0 0.144 251040.0 ; C4' O4'
11 13 2 gb_25 ;0.153 334720.0 0.153 334720.0 ; C4' C3'
12 19 2 gb_19 ;0.144 251040.0 0.144 251040.0 ; O4' C1'
13 14 2 gb_19 ;0.143 334720.0 0.143 334720.0 ; C3' O3'
13 16 2 gb_25 ;0.153 334720.0 0.153 334720.0 ; C3' C2'
14 15 2 gb_1 ;0.100 313800.0 0.100 313800.0 ; O3' HAA
16 17 2 gb_19 ;0.143 334720.0 0.143 334720.0 ; C2' O2'
16 19 2 gb_25 ;0.153 334720.0 0.153 334720.0 ; C2' C1'
17 18 2 gb_1 ;0.100 313800.0 0.100 313800.0 ; O2' HAB
19 20 2 gb_21 ;0.148 251040.0 0.148 251040.0 ; C1' N9
20 21 2 gb_9 ;0.133 418400.0 0.133 418400.0 ; N9 C8
20 24 2 gb_9 ;0.133 418400.0 0.133 418400.0 ; N9 C4
21 22 2 gb_9 ;0.133 418400.0 0.133 418400.0 ; C8 N7
22 23 2 gb_9 ;0.133 418400.0 0.133 418400.0 ; N7 C5
23 24 2 gb_15 ;0.139 418400.0 0.139 418400.0 ; C5 C4
23 32 2 gb_15 ;0.139 418400.0 0.139 418400.0 ; C5 C6
24 25 2 gb_11 ;0.134 418400.0 0.134 418400.0 ; C4 N3
25 26 2 gb_11 ;0.134 418400.0 0.134 418400.0 ; N3 C2
26 27 2 gb_8 ;0.133 376560.0 0.133 376560.0 ; C2 N2
26 30 2 gb_16 ;0.140 334720.0 0.140 334720.0 ; C2 N1
27 28 2 gb_2 ;0.100 374468.0 0.100 374468.0 ; N2 HAE
27 29 2 gb_2 ;0.100 374468.0 0.100 374468.0 ; N2 HAD
30 31 2 gb_2 ;0.100 374468.0 0.100 374468.0 ; N1 HAC
30 32 2 gb_16 ;0.140 334720.0 0.140 334720.0 ; N1 C6
32 33 2 gb_4 ;0.123 502080.0 0.123 502080.0 ; C6 O6
[ pairs ]
; ai aj fu c0, c1, ...
1 6 1 ; O2B PA
2 7 1 ; PB O1A
2 8 1 ; PB O2A
2 9 1 ; PB O5'
3 6 1 ; O3B PA
4 6 1 ; O1B PA
5 10 1 ; O3A C5'
6 11 1 ; PA C4'
7 10 1 ; O1A C5'
8 10 1 ; O2A C5'
9 12 1 ; O5' O4'
9 13 1 ; O5' C3'
10 14 1 ; C5' O3'
10 16 1 ; C5' C2'
10 19 1 ; C5' C1'
11 15 1 ; C4' HAA
11 17 1 ; C4' O2'
11 20 1 ; C4' N9
12 14 1 ; O4' O3'
12 17 1 ; O4' O2'
12 21 1 ; O4' C8
12 24 1 ; O4' C4
13 18 1 ; C3' HAB
13 20 1 ; C3' N9
14 17 1 ; O3' O2'
14 19 1 ; O3' C1'
15 16 1 ; HAA C2'
16 21 1 ; C2' C8
16 24 1 ; C2' C4
17 20 1 ; O2' N9
18 19 1 ; HAB C1'
19 22 1 ; C1' N7
19 23 1 ; C1' C5
19 25 1 ; C1' N3
20 26 1 ; N9 C2
20 32 1 ; N9 C6
21 25 1 ; C8 N3
21 32 1 ; C8 C6
22 25 1 ; N7 N3
22 30 1 ; N7 N1
22 33 1 ; N7 O6
23 26 1 ; C5 C2
23 31 1 ; C5 HAC
24 27 1 ; C4 N2
24 30 1 ; C4 N1
24 33 1 ; C4 O6
25 28 1 ; N3 HAE
25 29 1 ; N3 HAD
25 31 1 ; N3 HAC
25 32 1 ; N3 C6
26 33 1 ; C2 O6
27 31 1 ; N2 HAC
27 32 1 ; N2 C6
28 30 1 ; HAE N1
29 30 1 ; HAD N1
31 33 1 ; HAC O6
[ angles ]
; ai aj ak fu c0, c1, ...
1 2 3 2 ga_13 ;103.0 397.5 103.0 397.5 ; O2B PB O3B
1 2 4 2 ga_13 ;109.6 397.5 109.6 397.5 ; O2B PB O1B
1 2 5 2 ga_13 ;103.0 397.5 103.0 397.5 ; O2B PB O3A
3 2 4 2 ga_13 ;109.6 397.5 109.6 397.5 ; O3B PB O1B
3 2 5 2 ga_13 ;103.0 397.5 103.0 397.5 ; O3B PB O3A
4 2 5 2 ga_13 ;109.6 397.5 109.6 397.5 ; O1B PB O3A
2 5 6 2 ga_25 ;120.0 397.5 120.0 397.5 ; PB O3A PA
5 6 7 2 ga_13 ;109.6 397.5 109.6 397.5 ; O3A PA O1A
5 6 8 2 ga_13 ;109.6 397.5 109.6 397.5 ; O3A PA O2A
5 6 9 2 ga_4 ;103.0 397.5 103.0 397.5 ; O3A PA O5'
7 6 8 2 ga_28 ;120.0 585.8 120.0 585.8 ; O1A PA O2A
7 6 9 2 ga_13 ;109.6 397.5 109.6 397.5 ; O1A PA O5'
8 6 9 2 ga_13 ;109.6 397.5 109.6 397.5 ; O2A PA O5'
6 9 10 2 ga_25 ;120.0 397.5 120.0 397.5 ; PA O5' C5'
9 10 11 2 ga_8 ;111.0 460.2 111.0 460.2 ; O5' C5' C4'
10 11 12 2 ga_8 ;109.5 284.5 109.5 284.5 ; C5' C4' O4'
10 11 13 2 ga_7 ;109.5 251.0 109.5 251.0 ; C5' C4' C3'
12 11 13 2 ga_8 ;104.0 460.2 104.0 460.2 ; O4' C4' C3'
11 12 19 2 ga_9 ;104.0 460.2 104.0 460.2 ; C4' O4' C1'
11 13 14 2 ga_8 ;109.5 460.2 109.5 460.2 ; C4' C3' O3'
11 13 16 2 ga_7 ;104.0 460.2 104.0 460.2 ; C4' C3' C2'
14 13 16 2 ga_8 ;109.5 460.2 109.5 460.2 ; O3' C3' C2'
13 14 15 2 ga_11 ;109.5 397.5 109.5 397.5 ; C3' O3' HAA
13 16 17 2 ga_8 ;109.5 460.2 109.5 460.2 ; C3' C2' O2'
13 16 19 2 ga_7 ;104.0 460.2 104.0 460.2 ; C3' C2' C1'
17 16 19 2 ga_8 ;109.5 460.2 109.5 460.2 ; O2' C2' C1'
16 17 18 2 ga_11 ;109.5 397.5 109.5 397.5 ; C2' O2' HAB
12 19 16 2 ga_8 ;104.0 460.2 104.0 460.2 ; O4' C1' C2'
12 19 20 2 ga_8 ;109.5 284.5 109.5 284.5 ; O4' C1' N9
16 19 20 2 ga_8 ;109.5 284.5 109.5 284.5 ; C2' C1' N9
19 20 21 2 ga_36 ;126.0 418.4 126.0 418.4 ; C1' N9 C8
19 20 24 2 ga_36 ;126.0 418.4 126.0 418.4 ; C1' N9 C4
21 20 24 2 ga_6 ;108.0 418.4 108.0 418.4 ; C8 N9 C4
20 21 22 2 ga_6 ;108.0 418.4 108.0 418.4 ; N9 C8 N7
21 22 23 2 ga_6 ;108.0 418.4 108.0 418.4 ; C8 N7 C5
22 23 24 2 ga_6 ;108.0 418.4 108.0 418.4 ; N7 C5 C4
22 23 32 2 ga_38 ;132.0 418.4 132.0 418.4 ; N7 C5 C6
24 23 32 2 ga_26 ;120.0 418.4 120.0 418.4 ; C4 C5 C6
20 24 23 2 ga_6 ;108.0 418.4 108.0 418.4 ; N9 C4 C5
20 24 25 2 ga_38 ;132.0 418.4 132.0 418.4 ; N9 C4 N3
23 24 25 2 ga_26 ;120.0 418.4 120.0 418.4 ; C5 C4 N3
24 25 26 2 ga_26 ;120.0 418.4 120.0 418.4 ; C4 N3 C2
25 26 27 2 ga_26 ;120.0 418.4 120.0 418.4 ; N3 C2 N2
25 26 30 2 ga_26 ;120.0 418.4 120.0 418.4 ; N3 C2 N1
27 26 30 2 ga_26 ;120.0 418.4 120.0 418.4 ; N2 C2 N1
26 27 28 2 ga_22 ;120.0 292.9 120.0 292.9 ; C2 N2 HAE
26 27 29 2 ga_22 ;120.0 292.9 120.0 292.9 ; C2 N2 HAD
28 27 29 2 ga_23 ;120.0 334.7 120.0 334.7 ; HAE N2 HAD
26 30 31 2 ga_24 ;120.0 376.6 120.0 376.6 ; C2 N1 HAC
26 30 32 2 ga_26 ;120.0 418.4 120.0 418.4 ; C2 N1 C6
31 30 32 2 ga_24 ;120.0 376.6 120.0 376.6 ; HAC N1 C6
23 32 30 2 ga_26 ;120.0 418.4 120.0 418.4 ; C5 C6 N1
23 32 33 2 ga_26 ;120.0 418.4 120.0 418.4 ; C5 C6 O6
30 32 33 2 ga_26 ;120.0 418.4 120.0 418.4 ; N1 C6 O6
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
19 21 24 20 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp N9 C1' C8 C4
32 24 22 23 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp C5 C6 C4 N7
25 23 20 24 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp C4 N3 C5 N9
25 30 27 26 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp C2 N3 N1 N2
26 28 29 27 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp N2 C2 HAE HAD
32 31 26 30 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp N1 C6 HAC C2
23 30 33 32 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp C6 C5 N1 O6
1 4 3 2 2 gi_2 ; 35.3 836.8 0 35.3 836.8 0 ; imp PB O2B O1B O3B
5 8 7 6 2 gi_2 ; 35.3 836.8 0 35.3 836.8 0 ; imp PA O3A O2A O1A
10 13 12 11 2 gi_2 ; 35.3 836.8 0 35.3 836.8 0 ; imp C4' C5' C3' O4'
11 16 14 13 2 gi_2 ; 35.3 836.8 0 35.3 836.8 0 ; imp C3' C4' C2' O3'
13 19 17 16 2 gi_2 ; 35.3 836.8 0 35.3 836.8 0 ; imp C2' C3' C1' O2'
12 16 20 19 2 gi_2 ; 35.3 836.8 0 35.3 836.8 0 ; imp C1' O4' C2' N9
21 22 23 20 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp N9 C8 N7 C5
22 23 24 21 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp C8 N7 C5 C4
23 24 20 22 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp N7 C5 C4 N9
24 20 21 23 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp C5 C4 N9 C8
20 21 22 24 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp C4 N9 C8 N7
24 25 26 23 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp C5 C4 N3 C2
25 26 30 24 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp C4 N3 C2 N1
26 30 32 25 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp N3 C2 N1 C6
30 32 23 26 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp C2 N1 C6 C5
32 23 24 30 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp N1 C6 C5 C4
23 24 25 32 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp C6 C5 C4 N3
5 2 1 6 1 gd_11 ; 0.0 1.0 3 0.0 1.0 3 ; dih PA O3A PB O2B
5 2 1 6 1 gd_9 ; 0.0 3.1 2 0.0 3.1 2 ; dih PA O3A PB O2B
5 6 9 2 1 gd_11 ; 0.0 1.0 3 0.0 1.0 3 ; dih PB O3A PA O5'
5 6 9 2 1 gd_9 ; 0.0 3.1 2 0.0 3.1 2 ; dih PB O3A PA O5'
9 6 5 10 1 gd_9 ; 0.0 1.0 3 0.0 1.0 3 ; dih C5' O5' PA O3A
9 6 5 10 1 gd_11 ; 0.0 3.1 2 0.0 3.1 2 ; dih C5' O5' PA O3A
9 10 11 6 1 gd_14 ; 0.0 3.8 3 0.0 3.8 3 ; dih PA O5' C5' C4'
11 10 9 13 1 gd_7 ; 0.0 5.9 3 0.0 5.9 3 ; dih C3' C4' C5' O5'
11 12 19 10 1 gd_14 ; 0.0 3.8 3 0.0 3.8 3 ; dih C5' C4' O4' C1'
11 13 16 10 1 gd_17 ; 0.0 5.9 3 0.0 5.9 3 ; dih C5' C4' C3' C2'
19 12 11 20 1 gd_14 ; 0.0 3.8 3 0.0 3.8 3 ; dih N9 C1' O4' C4'
13 14 15 11 1 gd_12 ; 0.0 1.3 3 0.0 1.3 3 ; dih C4' C3' O3' HAA
16 13 11 19 1 gd_17 ; 0.0 5.9 3 0.0 5.9 3 ; dih C1' C2' C3' C4'
16 17 18 13 1 gd_12 ; 0.0 1.3 3 0.0 1.3 3 ; dih C3' C2' O2' HAB
16 19 20 13 1 gd_7 ; 0.0 5.9 3 0.0 5.9 3 ; dih C3' C2' C1' N9
19 20 24 12 1 gd_6 ; 0.0 0.0 2 0.0 0.0 2 ; dih O4' C1' N9 C4
26 27 29 25 1 gd_4 ;180.0 33.5 2 180.0 33.5 2 ; dih N3 C2 N2 HAD
; Include Position restraint file
#ifdef POSRES_GDP
#include "posre_gdp.itp"
#endif
; Include water topology
#include "spc.itp"
; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
GDP in water
[ molecules ]
; Compound #mols
GDP 1
SOL 1838
-------------------------------------------------------------------------------
EM_gdp.mdp
-------------------------------------------------------------------------------
title = mitwasser
cpp = /lib/cpp
define = -DFLEXIBLE -DPOSRES_GDP
constraints = none
integrator = l-bfgs
dt = 0.002 ; ps !
nsteps = 5000
nstlist = 5 ;originally this is set to 10
ns_type = grid
coulombtype = Switch
vdw-type = Switch
rlist = 1.2
rcoulomb = 1.0
rvdw = 1.0
;http://www.gromacs.org/pipermail/gmx-users/2004-May/010608.html
; Energy minimizing stuff
;
emtol = 10.0
emstep = 0.01
epsilon_r = 1
-------------------------------------------------------------------------------
Deformed_gdp.pdb
-------------------------------------------------------------------------------
HEADER GDP in water
MODEL 1
ATOM 1 O2B GDP 1 24.340 16.030 15.246 1.00 0.00
ATOM 2 PB GDP 1 25.390 17.010 15.440 1.00 0.00
ATOM 3 O3B GDP 1 26.840 16.840 15.446 1.00 0.00
ATOM 4 O1B GDP 1 25.250 18.190 14.580 1.00 0.00
ATOM 5 O3A GDP 1 24.990 17.830 16.606 1.00 0.00
ATOM 6 PA GDP 1 25.280 16.740 17.586 1.00 0.00
ATOM 7 O1A GDP 1 24.060 16.120 18.146 1.00 0.00
ATOM 8 O2A GDP 1 26.540 16.800 18.360 1.00 0.00
ATOM 9 O5' GDP 1 25.050 17.730 18.860 1.00 0.00
ATOM 10 C5' GDP 1 24.480 19.060 18.866 1.00 0.00
ATOM 11 C4' GDP 1 23.090 18.920 19.460 1.00 0.00
ATOM 12 O4' GDP 1 22.040 18.880 18.480 1.00 0.00
ATOM 13 C3' GDP 1 22.690 19.970 20.500 1.00 0.00
ATOM 14 O3' GDP 1 23.340 19.900 21.820 1.00 0.00
ATOM 15 HAA GDP 1 24.330 20.130 21.720 1.00 0.00
ATOM 16 C2' GDP 1 21.150 19.890 20.280 1.00 0.00
ATOM 17 O2' GDP 1 20.310 19.760 21.440 1.00 0.00
ATOM 18 HAB GDP 1 19.750 20.600 21.480 1.00 0.00
ATOM 19 C1' GDP 1 21.070 18.600 19.480 1.00 0.00
ATOM 20 N9 GDP 1 20.040 17.610 19.046 1.00 0.00
ATOM 21 C8 GDP 1 20.430 16.580 18.280 1.00 0.00
ATOM 22 N7 GDP 1 19.510 15.630 18.286 1.00 0.00
ATOM 23 C5 GDP 1 18.500 16.110 19.046 1.00 0.00
ATOM 24 C4 GDP 1 18.770 17.430 19.526 1.00 0.00
ATOM 25 N3 GDP 1 17.600 18.240 20.140 1.00 0.00
ATOM 26 C2 GDP 1 16.620 17.910 19.380 1.00 0.00
ATOM 27 N2 GDP 1 16.220 18.220 20.286 1.00 0.00
ATOM 28 HAE GDP 1 17.430 18.290 20.226 1.00 0.00
ATOM 29 HAD GDP 1 15.300 18.360 20.706 1.00 0.00
ATOM 30 N1 GDP 1 16.200 16.710 19.266 1.00 0.00
ATOM 31 HAC GDP 1 15.320 16.520 19.640 1.00 0.00
ATOM 32 C6 GDP 1 17.140 15.770 19.166 1.00 0.00
ATOM 33 O6 GDP 1 16.710 14.660 19.460 1.00 0.00
TER 34 GDP 1
ENDMDL
END
-------------------------------------------------------------------------------
Yours sincerely,
Zhenting Gao
zhentg at 163.com
2004-11-3
------------------------------------
Drug Discovery and Design Center,
Shanghai Institute of Materia Medica,
Chinese Academy of Science
P.R. China
URL http://www.dddc.ac.cn/group/zhentg.htm
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