"Broken bonds" are probably a visualization artefact. Did you try what
I suggested about minimizing just DPPC? Better yet, try minimizing one
single DPPC molecule in vacuo to see if that succeeds, then move up to
the bilayer, etc.
Also, increasing the table-extension is usually not going to solve
anything. If you're system is exploding, it's going to explode no
matter what the table-extension is.
-Justin
serdar durdagi wrote:
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 [EMAIL PROTECTED]
;
; 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
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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