[gmx-users] lipid itp problem
serdar durdagi
durdagis at yahoo.de
Mon Jul 7 12:47:27 CEST 2008
Dear all,
Sorry for the previous e-mail format. I am writing again the problem.
I am trying to simulate drug at the binding site of the receptor surrounded by DPPC bilayer system. I have problem at the energy minimisation step. Always, I am getting below error message:
Warning: 1-4 interaction between 3642 and 3647 at distance 1.325 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file
Step= 0, Dmax= 1.0e-02 nm, Epot= 7.16584e+15 Fmax= 5.29841e+18, atom= 2662 Step= 1, Dmax= 1.0e-02 nm, Epot= 1.19114e+12 Fmax= 2.10320e+14, atom= 3605 Step= 2, Dmax= 1.2e-02 nm, Epot= 1.39843e+10 Fmax= 8.84756e+11, atom= 2662 Step= 3, Dmax= 1.4e-02 nm, Epot= 1.36040e+09 Fmax= 5.31692e+10, atom= 2661
When I try to increase table-extension to more than 1.0, 1-4 interaction always increases.
I checked the *.gro file, it seems during the minimisation, bonds at protein and drg molecules are fine however, bonds at the DPPC molecules are broken.
I guess problem is at the *.itp file of dppc. I produced *.itp file of DPPC from PRODRG. *itp file of lipid and *.mdp file for energy minimisation are attached below. Could any body give a clue for the solution? Many thanks in advanced.
Serdar Durdagi
;
;
; This file was generated by PRODRG version 071121.0636
; PRODRG written/copyrighted by Daan van Aalten
; and Alexander Schuettelkopf
;
; 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.
;
;
[ moleculetype ]
; Name nrexcl
MOL 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 CH3 1 MOL C8 1 -0.033 15.0350
2 CH2 1 MOL C1 1 0.008 14.0270
3 CH2 1 MOL C45 1 0.008 14.0270
4 CH2 1 MOL C44 1 0.009 14.0270
5 CH2 1 MOL C43 1 0.008 14.0270
6 CH2 1 MOL C42 2 0.000 14.0270
7 CH2 1 MOL C41 2 0.000 14.0270
8 CH2 1 MOL C40 3 0.000 14.0270
9 CH2 1 MOL C39 3 0.000 14.0270
10 CH2 1 MOL C38 4 0.000 14.0270
11 CH2 1 MOL C37 4 0.000 14.0270
12 CH2 1 MOL C36 5 0.000 14.0270
13 CH2 1 MOL C35 5 0.000 14.0270
14 CH2 1 MOL C34 6 0.000 14.0270
15 CH2 1 MOL C33 7 0.036 14.0270
16 C 1 MOL C32 7 0.438 12.0110
17 O 1 MOL O46 7 -0.551 15.9994
18 OS 1 MOL O31 7 -0.160 15.9994
19 CS1 1 MOL C13 7 0.237 13.0190
20 CH2 1 MOL C12 8 0.000 14.0270
21 OS 1 MOL O11 9 -0.256 15.9994
22 P 1 MOL P8 9 0.998 30.9738
23 OM 1 MOL O10 9 -0.743 15.9994
24 OM 1 MOL O9 9 -0.743 15.9994
25 OS 1 MOL O4 9 -0.256 15.9994
26 CH2 1 MOL C3 10 0.041 14.0270
27 CH2 1 MOL C2 10 0.041 14.0270
28 NL 1 MOL N1 10 0.918 14.0067
29 CH3 1 MOL C6 11 0.000 15.0350
30 CH3 1 MOL C5 11 0.000 15.0350
31 CH3 1 MOL C7 12 0.000 15.0350
32 CS2 1 MOL C14 13 0.242 14.0270
33 OS 1 MOL O15 13 -0.162 15.9994
34 C 1 MOL C16 13 0.437 12.0110
35 O 1 MOL O30 13 -0.553 15.9994
36 CH2 1 MOL C17 13 0.036 14.0270
37 CH2 1 MOL C18 14 0.000 14.0270
38 CH2 1 MOL C19 14 0.000 14.0270
39 CH2 1 MOL C20 15 0.000 14.0270
40 CH2 1 MOL C21 15 0.000 14.0270
41 CH2 1 MOL C22 16 0.000 14.0270
42 CH2 1 MOL C23 16 0.000 14.0270
43 CH2 1 MOL C24 17 0.000 14.0270
44 CH2 1 MOL C25 17 0.000 14.0270
45 CH2 1 MOL C26 18 0.000 14.0270
46 CH2 1 MOL C27 19 0.008 14.0270
47 CH2 1 MOL C28 19 0.008 14.0270
48 CH2 1 MOL C29 19 0.008 14.0270
49 CH2 1 MOL C9 19 0.009 14.0270
50 CH3 1 MOL C10 19 -0.033 15.0350
[ bonds ]
; ai aj fu c0, c1, ...
1 2 1 0.153 334720.0 0.153 334720.0 ; C8 C1
2 3 1 0.153 334720.0 0.153 334720.0 ; C1 C45
3 4 1 0.153 334720.0 0.153 334720.0 ; C45 C44
4 5 1 0.153 334720.0 0.153 334720.0 ; C44 C43
5 6 1 0.153 334720.0 0.153 334720.0 ; C43 C42
6 7 1 0.153 334720.0 0.153 334720.0 ; C42 C41
7 8 1 0.153 334720.0 0.153 334720.0 ; C41 C40
8 9 1 0.153 334720.0 0.153 334720.0 ; C40 C39
9 10 1 0.153 334720.0 0.153 334720.0 ; C39 C38
10 11 1 0.153 334720.0 0.153 334720.0 ; C38 C37
11 12 1 0.153 334720.0 0.153 334720.0 ; C37 C36
12 13 1 0.153 334720.0 0.153 334720.0 ; C36 C35
13 14 1 0.153 334720.0 0.153 334720.0 ; C35 C34
14 15 1 0.153 334720.0 0.153 334720.0 ; C34 C33
15 16 1 0.153 334720.0 0.153 334720.0 ; C33 C32
16 17 1 0.123 502080.0 0.123 502080.0 ; C32 O46
16 18 1 0.136 376560.0 0.136 376560.0 ; C32 O31
18 19 1 0.144 251040.0 0.144 251040.0 ; O31 C13
19 20 1 0.153 251040.0 0.153 251040.0 ; C13 C12
19 32 1 0.152 251040.0 0.152 251040.0 ; C13 C14
20 21 1 0.143 251040.0 0.143 251040.0 ; C12 O11
21 22 1 0.161 251040.0 0.161 251040.0 ; O11 P8
22 23 1 0.148 376560.0 0.148 376560.0 ; P8 O10
22 24 1 0.148 376560.0 0.148 376560.0 ; P8 O9
22 25 1 0.161 251040.0 0.161 251040.0 ; P8 O4
25 26 1 0.143 251040.0 0.143 251040.0 ; O4 C3
26 27 1 0.153 334720.0 0.153 334720.0 ; C3 C2
27 28 1 0.147 376560.0 0.147 376560.0 ; C2 N1
28 29 1 0.147 376560.0 0.147 376560.0 ; N1 C6
28 30 1 0.147 376560.0 0.147 376560.0 ; N1 C5
28 31 1 0.147 376560.0 0.147 376560.0 ; N1 C7
32 33 1 0.144 251040.0 0.144 251040.0 ; C14 O15
33 34 1 0.136 376560.0 0.136 376560.0 ; O15 C16
34 35 1 0.123 502080.0 0.123 502080.0 ; C16 O30
34 36 1 0.153 334720.0 0.153 334720.0 ; C16 C17
36 37 1 0.153 334720.0 0.153 334720.0 ; C17 C18
37 38 1 0.153 334720.0 0.153 334720.0 ; C18 C19
38 39 1 0.153 334720.0 0.153 334720.0 ; C19 C20
39 40 1 0.153 334720.0 0.153 334720.0 ; C20 C21
40 41 1 0.153 334720.0 0.153 334720.0 ; C21 C22
41 42 1 0.153 334720.0 0.153 334720.0 ; C22 C23
42 43 1 0.153 334720.0 0.153 334720.0 ; C23 C24
43 44 1 0.153 334720.0 0.153 334720.0 ; C24 C25
44 45 1 0.153 334720.0 0.153 334720.0 ; C25 C26
45 46 1 0.153 334720.0 0.153 334720.0 ; C26 C27
46 47 1 0.153 334720.0 0.153 334720.0 ; C27 C28
47 48 1 0.153 334720.0 0.153 334720.0 ; C28 C29
48 49 1 0.153 334720.0 0.153 334720.0 ; C29 C9
49 50 1 0.153 334720.0 0.153 334720.0 ; C9 C10
[ pairs ]
; ai aj fu c0, c1, ...
1 4 1 ; C8 C44
2 5 1 ; C1 C43
3 6 1 ; C45 C42
4 7 1 ; C44 C41
5 8 1 ; C43 C40
6 9 1 ; C42 C39
7 10 1 ; C41 C38
8 11 1 ; C40 C37
9 12 1 ; C39 C36
10 13 1 ; C38 C35
11 14 1 ; C37 C34
12 15 1 ; C36 C33
13 16 1 ; C35 C32
14 17 1 ; C34 O46
14 18 1 ; C34 O31
15 19 1 ; C33 C13
16 20 1 ; C32 C12
16 32 1 ; C32 C14
17 19 1 ; O46 C13
18 21 1 ; O31 O11
18 33 1 ; O31 O15
19 22 1 ; C13 P8
19 34 1 ; C13 C16
20 23 1 ; C12 O10
20 24 1 ; C12 O9
20 25 1 ; C12 O4
20 33 1 ; C12 O15
21 26 1 ; O11 C3
21 32 1 ; O11 C14
22 27 1 ; P8 C2
23 26 1 ; O10 C3
24 26 1 ; O9 C3
25 28 1 ; O4 N1
26 29 1 ; C3 C6
26 30 1 ; C3 C5
26 31 1 ; C3 C7
32 35 1 ; C14 O30
32 36 1 ; C14 C17
33 37 1 ; O15 C18
34 38 1 ; C16 C19
35 37 1 ; O30 C18
36 39 1 ; C17 C20
37 40 1 ; C18 C21
38 41 1 ; C19 C22
39 42 1 ; C20 C23
40 43 1 ; C21 C24
41 44 1 ; C22 C25
42 45 1 ; C23 C26
43 46 1 ; C24 C27
44 47 1 ; C25 C28
45 48 1 ; C26 C29
46 49 1 ; C27 C9
47 50 1 ; C28 C10
[ angles ]
; ai aj ak fu c0, c1, ...
1 2 3 1 111.0 460.2 111.0 460.2 ; C8 C1 C45
2 3 4 1 111.0 460.2 111.0 460.2 ; C1 C45 C44
3 4 5 1 111.0 460.2 111.0 460.2 ; C45 C44 C43
4 5 6 1 111.0 460.2 111.0 460.2 ; C44 C43 C42
5 6 7 1 111.0 460.2 111.0 460.2 ; C43 C42 C41
6 7 8 1 111.0 460.2 111.0 460.2 ; C42 C41 C40
7 8 9 1 111.0 460.2 111.0 460.2 ; C41 C40 C39
8 9 10 1 111.0 460.2 111.0 460.2 ; C40 C39 C38
9 10 11 1 111.0 460.2 111.0 460.2 ; C39 C38 C37
10 11 12 1 111.0 460.2 111.0 460.2 ; C38 C37 C36
11 12 13 1 111.0 460.2 111.0 460.2 ; C37 C36 C35
12 13 14 1 111.0 460.2 111.0 460.2 ; C36 C35 C34
13 14 15 1 111.0 460.2 111.0 460.2 ; C35 C34 C33
14 15 16 1 111.0 460.2 111.0 460.2 ; C34 C33 C32
15 16 17 1 121.0 502.1 121.0 502.1 ; C33 C32 O46
15 16 18 1 120.0 418.4 120.0 418.4 ; C33 C32 O31
17 16 18 1 120.0 418.4 120.0 418.4 ; O46 C32 O31
16 18 19 1 109.5 334.7 109.5 334.7 ; C32 O31 C13
18 19 20 1 109.5 284.5 109.5 284.5 ; O31 C13 C12
18 19 32 1 109.5 284.5 109.5 284.5 ; O31 C13 C14
20 19 32 1 109.5 251.0 109.5 251.0 ; C12 C13 C14
19 20 21 1 111.0 460.2 111.0 460.2 ; C13 C12 O11
20 21 22 1 120.0 397.5 120.0 397.5 ; C12 O11 P8
21 22 23 1 109.6 397.5 109.6 397.5 ; O11 P8 O10
21 22 24 1 109.6 397.5 109.6 397.5 ; O11 P8 O9
21 22 25 1 103.0 397.5 103.0 397.5 ; O11 P8 O4
23 22 24 1 120.0 585.8 120.0 585.8 ; O10 P8 O9
23 22 25 1 109.6 397.5 109.6 397.5 ; O10 P8 O4
24 22 25 1 109.6 397.5 109.6 397.5 ; O9 P8 O4
22 25 26 1 120.0 397.5 120.0 397.5 ; P8 O4 C3
25 26 27 1 109.5 460.2 109.5 460.2 ; O4 C3 C2
26 27 28 1 109.5 460.2 109.5 460.2 ; C3 C2 N1
27 28 29 1 109.5 376.6 109.5 376.6 ; C2 N1 C6
27 28 30 1 109.5 376.6 109.5 376.6 ; C2 N1 C5
27 28 31 1 109.5 376.6 109.5 376.6 ; C2 N1 C7
29 28 30 1 109.5 376.6 109.5 376.6 ; C6 N1 C5
29 28 31 1 109.5 376.6 109.5 376.6 ; C6 N1 C7
30 28 31 1 109.5 376.6 109.5 376.6 ; C5 N1 C7
19 32 33 1 109.5 284.5 109.5 284.5 ; C13 C14 O15
32 33 34 1 109.5 334.7 109.5 334.7 ; C14 O15 C16
33 34 35 1 120.0 418.4 120.0 418.4 ; O15 C16 O30
33 34 36 1 120.0 418.4 120.0 418.4 ; O15 C16 C17
35 34 36 1 121.0 502.1 121.0 502.1 ; O30 C16 C17
34 36 37 1 111.0 460.2 111.0 460.2 ; C16 C17 C18
36 37 38 1 111.0 460.2 111.0 460.2 ; C17 C18 C19
37 38 39 1 111.0 460.2 111.0 460.2 ; C18 C19 C20
38 39 40 1 111.0 460.2 111.0 460.2 ; C19 C20 C21
39 40 41 1 111.0 460.2 111.0 460.2 ; C20 C21 C22
40 41 42 1 111.0 460.2 111.0 460.2 ; C21 C22 C23
41 42 43 1 111.0 460.2 111.0 460.2 ; C22 C23 C24
42 43 44 1 111.0 460.2 111.0 460.2 ; C23 C24 C25
43 44 45 1 111.0 460.2 111.0 460.2 ; C24 C25 C26
44 45 46 1 111.0 460.2 111.0 460.2 ; C25 C26 C27
45 46 47 1 111.0 460.2 111.0 460.2 ; C26 C27 C28
46 47 48 1 111.0 460.2 111.0 460.2 ; C27 C28 C29
47 48 49 1 111.0 460.2 111.0 460.2 ; C28 C29 C9
48 49 50 1 111.0 460.2 111.0 460.2 ; C29 C9 C10
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
16 15 18 17 2 0.0 1673.6 0.0 1673.6 ; imp C32 C33 O31 O46
34 33 36 35 2 0.0 1673.6 0.0 1673.6 ; imp C16 O15 C17 O30
19 18 32 20 2 35.3 836.8 35.3 836.8 ; imp C13 O31 C14 C12
22 21 24 23 2 35.3 836.8 35.3 836.8 ; imp P8 O11 O9 O10
28 27 29 30 2 35.3 836.8 35.3 836.8 ; imp N1 C2 C6 C5
4 3 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih C44 C45 C1 C8
5 4 3 2 1 0.0 5.9 3 0.0 5.9 3 ; dih C43 C44 C45 C1
6 5 4 3 1 0.0 5.9 3 0.0 5.9 3 ; dih C42 C43 C44 C45
7 6 5 4 1 0.0 5.9 3 0.0 5.9 3 ; dih C41 C42 C43 C44
8 7 6 5 1 0.0 5.9 3 0.0 5.9 3 ; dih C40 C41 C42 C43
9 8 7 6 1 0.0 5.9 3 0.0 5.9 3 ; dih C39 C40 C41 C42
10 9 8 7 1 0.0 5.9 3 0.0 5.9 3 ; dih C38 C39 C40 C41
11 10 9 8 1 0.0 5.9 3 0.0 5.9 3 ; dih C37 C38 C39 C40
12 11 10 9 1 0.0 5.9 3 0.0 5.9 3 ; dih C36 C37 C38 C39
13 12 11 10 1 0.0 5.9 3 0.0 5.9 3 ; dih C35 C36 C37 C38
14 13 12 11 1 0.0 5.9 3 0.0 5.9 3 ; dih C34 C35 C36 C37
15 14 13 12 1 0.0 5.9 3 0.0 5.9 3 ; dih C33 C34 C35 C36
16 15 14 13 1 0.0 5.9 3 0.0 5.9 3 ; dih C32 C33 C34 C35
14 15 16 18 1 0.0 0.4 6 0.0 0.4 6 ; dih C34 C33 C32 O31
15 16 18 19 1 180.0 16.7 2 180.0 16.7 2 ; dih C33 C32 O31 C13
32 19 18 16 1 0.0 3.8 3 0.0 3.8 3 ; dih C14 C13 O31 C32
18 19 20 21 1 0.0 5.9 3 0.0 5.9 3 ; dih O31 C13 C12 O11
33 32 19 18 1 0.0 5.9 3 0.0 5.9 3 ; dih O15 C14 C13 O31
22 21 20 19 1 0.0 3.8 3 0.0 3.8 3 ; dih P8 O11 C12 C13
20 21 22 25 1 0.0 1.0 3 0.0 1.0 3 ; dih C12 O11 P8 O4
20 21 22 25 1 0.0 3.1 2 0.0 3.1 2 ; dih C12 O11 P8 O4
26 25 22 21 1 0.0 1.0 3 0.0 1.0 3 ; dih C3 O4 P8 O11
26 25 22 21 1 0.0 3.1 2 0.0 3.1 2 ; dih C3 O4 P8 O11
22 25 26 27 1 0.0 3.8 3 0.0 3.8 3 ; dih P8 O4 C3 C2
28 27 26 25 1 0.0 5.9 3 0.0 5.9 3 ; dih N1 C2 C3 O4
26 27 28 31 1 0.0 3.8 3 0.0 3.8 3 ; dih C3 C2 N1 C7
19 32 33 34 1 0.0 3.8 3 0.0 3.8 3 ; dih C13 C14 O15 C16
32 33 34 36 1 180.0 16.7 2 180.0 16.7 2 ; dih C14 O15 C16 C17
37 36 34 33 1 0.0 0.4 6 0.0 0.4 6 ; dih C18 C17 C16 O15
38 37 36 34 1 0.0 5.9 3 0.0 5.9 3 ; dih C19 C18 C17 C16
39 38 37 36 1 0.0 5.9 3 0.0 5.9 3 ; dih C20 C19 C18 C17
40 39 38 37 1 0.0 5.9 3 0.0 5.9 3 ; dih C21 C20 C19 C18
41 40 39 38 1 0.0 5.9 3 0.0 5.9 3 ; dih C22 C21 C20 C19
42 41 40 39 1 0.0 5.9 3 0.0 5.9 3 ; dih C23 C22 C21 C20
43 42 41 40 1 0.0 5.9 3 0.0 5.9 3 ; dih C24 C23 C22 C21
44 43 42 41 1 0.0 5.9 3 0.0 5.9 3 ; dih C25 C24 C23 C22
45 44 43 42 1 0.0 5.9 3 0.0 5.9 3 ; dih C26 C25 C24 C23
46 45 44 43 1 0.0 5.9 3 0.0 5.9 3 ; dih C27 C26 C25 C24
47 46 45 44 1 0.0 5.9 3 0.0 5.9 3 ; dih C28 C27 C26 C25
48 47 46 45 1 0.0 5.9 3 0.0 5.9 3 ; dih C29 C28 C27 C26
49 48 47 46 1 0.0 5.9 3 0.0 5.9 3 ; dih C9 C29 C28 C27
50 49 48 47 1 0.0 5.9 3 0.0 5.9 3 ; dih C10 C9 C29 C28
title = vals
cpp = /usr/bin/cpp
define = -DFLEXIBLE
constraints = none
integrator = steep
dt = 0.002 ; ps !
nsteps = 500
nstlists = 10
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
;
; Energy minimizing
;
emtol = 100.0
emsteps = 0.01
__________________________________________________________
Gesendet von Yahoo! Mail.
Dem pfiffigeren Posteingang.
http://de.overview.mail.yahoo.com
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080707/94cda4c4/attachment.html>
More information about the gromacs.org_gmx-users
mailing list