There is nothing remarkable here, it looks to be a few changes in atom type
relative to DMPC, a procedure that I know has been used successfully for
DPPC:DPPE mixtures: dx.doi.org/10.1529/biophysj.105.076596
I stand by my previous reply. When analyzing your data, you have to consider
the innately different chemistry between DMPC and DMPE, particularly the
headgroups. I also would not draw any conclusions about the data generated
without a good set of controls (lipid only, no protein). I would also not
expect two different lipids to have the same influence on a bound protein.
-Justin
Kirill Bessonov wrote:
DMPE.itp file as attached
[ moleculetype ]
; Name nrexcl
DMPE 3
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 H 1 DMPE H1 0 0.4000
1.0080 ; qtot:0.36
2 H 1 DMPE H2 0 0.4000
1.0080 ; qtot:0.72
3 H 1 DMPE H3 0 0.4000
1.0008 ; qtot:1.08
4 LNL 1 DMPE N4 0 -0.5000 14.0067
; qtot:0.76
5 LH2 1 DMPE C5 0 0.3000
14.0270 ; qtot:1.0
6 LC2 1 DMPE C6 1 0.4000
14.0270 ; qtot:1.0
7 LOS 1 DMPE O7 1 -0.800
15.9994 ; qtot:0.54
8 LP 1 DMPE P8 1 1.700
30.9738 ; qtot:2.3
9 LOM 1 DMPE O9 1 -0.800
15.9994 ; qtot:1.5
10 LOM 1 DMPE O10 1 -0.800
15.9994 ; qtot:0.7
11 LOS 1 DMPE O11 1 -0.700
15.9994 ; qtot:0
12 LC2 1 DMPE C12 2 0.400
14.0270 ; qtot:0.08
13 LH1 1 DMPE C13 2 0.300
13.0190 ; qtot:0.52
14 LOS 1 DMPE O14 2 -0.700
15.9994 ; qtot:-0.14
15 LC 1 DMPE C15 2 0.7000
12.0110 ; qtot:0.56
16 LO 1 DMPE O16 2 -0.700
15.9994 ; qtot:0.0
17 LP2 1 DMPE C17 3 0.0
14.0270 ; qtot:
18 LP2 1 DMPE C18 4 0
14.0270 ; qtot:
19 LP2 1 DMPE C19 5 0
14.0270 ; qtot:
20 LP2 1 DMPE C20 6 0
14.0270 ; qtot:
21 LP2 1 DMPE C21 7 0
14.0270 ; qtot:
22 LP2 1 DMPE C22 8 0
14.0270 ; qtot:
23 LP2 1 DMPE C23 9 0
14.0270 ; qtot:
24 LP2 1 DMPE C24 10 0
14.0270 ; qtot:
25 LP2 1 DMPE C25 11 0
14.0270 ; qtot:
26 LP2 1 DMPE C26 12 0
14.0270 ; qtot:
27 LP2 1 DMPE C27 13 0
14.0270 ; qtot:
28 LP2 1 DMPE C28 14 0
14.0270 ; qtot:
29 LP3 1 DMPE C29 15 0
15.0350 ; qtot:
30 LC2 1 DMPE C32 16 0.50
14.0270 ; qtot:
31 LOS 1 DMPE O33 16 -0.70
15.9994 ; qtot:
32 LC 1 DMPE C34 16 0.80
12.0110 ; qtot:
33 LO 1 DMPE O35 16 -0.60
15.9994 ; qtot:
34 LP2 1 DMPE C36 17 0
14.0270 ; qtot:
35 LP2 1 DMPE C37 18 0
14.0270 ; qtot:
36 LP2 1 DMPE C38 19 0
14.0270 ; qtot:
37 LP2 1 DMPE C39 20 0
14.0270 ; qtot:
38 LP2 1 DMPE C40 21 0
14.0270 ; qtot:
39 LP2 1 DMPE C41 22 0
14.0270 ; qtot:
40 LP2 1 DMPE C42 23 0
14.0270 ; qtot:
41 LP2 1 DMPE C43 24 0
14.0270 ; qtot:
42 LP2 1 DMPE C44 25 0
14.0270 ; qtot:
43 LP2 1 DMPE C45 26 0
14.0270 ; qtot:
44 LP2 1 DMPE C46 27 0
14.0270 ; qtot:
45 LP2 1 DMPE C47 28 0
14.0270 ; qtot:
46 LP3 1 DMPE C48 29 0
15.0350 ; tail:
[ bonds ]
; ai aj funct
1 4 1 0.10000E+00 0.37450E+06
2 4 1 0.10000E+00 0.37450E+06
3 4 1 0.10000E+00 0.37450E+06
4 5 1 0.14700E+00 0.37660E+06
5 6 1 0.15300E+00 0.33470E+06
6 7 1 0.14300E+00 0.25100E+06
7 8 1 0.16100E+00 0.25100E+06
8 9 1 0.14800E+00 0.37660E+06
8 10 1 0.14800E+00 0.37660E+06
8 11 1 0.16100E+00 0.25100E+06
11 12 1 0.14300E+00 0.25100E+06
12 13 1 0.15300E+00 0.33470E+06
13 14 1 0.14350E+00 0.25100E+06
13 30 1 0.15300E+00 0.33470E+06
14 15 1 0.13600E+00 0.37660E+06
15 16 1 0.12300E+00 0.50210E+06
15 17 1 0.15300E+00 0.33470E+06
17 18 1 0.15300E+00 0.33470E+06
18 19 1 0.15300E+00 0.33470E+06
19 20 1 0.15300E+00 0.33470E+06
20 21 1 0.15300E+00 0.33470E+06
21 22 1 0.15300E+00 0.33470E+06
22 23 1 0.15300E+00 0.33470E+06
23 24 1 0.15300E+00 0.33470E+06
24 25 1 0.15300E+00 0.33470E+06
25 26 1 0.15300E+00 0.33470E+06
26 27 1 0.15300E+00 0.33470E+06
27 28 1 0.15300E+00 0.33470E+06
28 29 1 0.15300E+00 0.33470E+06
30 31 1 0.14300E+00 0.25100E+06
31 32 1 0.13600E+00 0.37660E+06
32 33 1 0.12300E+00 0.50210E+06
32 34 1 0.15300E+00 0.33470E+06
34 35 1 0.15300E+00 0.33470E+06
35 36 1 0.15300E+00 0.33470E+06
36 37 1 0.15300E+00 0.33470E+06
37 38 1 0.15300E+00 0.33470E+06
38 39 1 0.15300E+00 0.33470E+06
39 40 1 0.15300E+00 0.33470E+06
40 41 1 0.15300E+00 0.33470E+06
41 42 1 0.15300E+00 0.33470E+06
42 43 1 0.15300E+00 0.33470E+06
43 44 1 0.15300E+00 0.33470E+06
44 45 1 0.15300E+00 0.33470E+06
45 46 1 0.15300E+00 0.33470E+06
[ pairs ]
; ai aj funct
4 7 1
5 8 1
6 9 1
6 10 1
6 11 1
7 12 1
8 13 1
9 12 1
10 12 1
11 14 1
11 30 1
12 15 1
12 31 1
13 16 1
13 17 1
13 32 1
14 18 1
14 31 1
15 19 1
15 30 1
16 18 1
30 33 1
30 34 1
31 35 1
32 36 1
33 35 1
[ angles ]
; ai aj ak funct
4 5 6 1 0.10950E+03 0.46020E+03
5 6 7 1 0.10950E+03 0.46020E+03
6 7 8 1 0.12000E+03 0.39750E+03
7 8 9 1 0.10960E+03 0.39750E+03
7 8 10 1 0.10960E+03 0.39750E+03
7 8 11 1 0.10300E+03 0.39750E+03
8 11 12 1 0.12000E+03 0.39750E+03
9 8 10 1 0.12000E+03 0.58580E+03
9 8 11 1 0.10960E+03 0.39750E+03
10 8 11 1 0.10960E+03 0.39750E+03
11 12 13 1 0.11100E+03 0.46020E+03
12 13 14 1 0.10950E+03 0.46020E+03
12 13 32 1 0.10950E+03 0.46020E+03
13 14 15 1 0.12000E+03 0.41840E+03
13 30 31 1 0.11100E+03 0.46020E+03
14 13 30 1 0.10950E+03 0.46020E+03
14 15 16 1 0.12400E+03 0.50210E+03
14 15 17 1 0.11500E+03 0.50210E+03
15 17 18 1 0.11100E+03 0.46020E+03
16 15 17 1 0.12100E+03 0.50210E+03
17 18 19 1 0.11100E+03 0.46020E+03
18 19 20 1 0.11100E+03 0.46020E+03
19 20 21 1 0.11100E+03 0.46020E+03
20 21 22 1 0.11100E+03 0.46020E+03
21 22 23 1 0.11100E+03 0.46020E+03
22 23 24 1 0.11100E+03 0.46020E+03
23 24 25 1 0.11100E+03 0.46020E+03
24 25 26 1 0.11100E+03 0.46020E+03
25 26 27 1 0.11100E+03 0.46020E+03
26 27 28 1 0.11100E+03 0.46020E+03
27 28 29 1 0.11100E+03 0.46020E+03
30 31 32 1 0.12000E+03 0.41840E+03
31 32 33 1 0.12400E+03 0.50210E+03
31 32 34 1 0.11500E+03 0.50210E+03
32 34 35 1 0.11100E+03 0.46020E+03
33 32 34 1 0.12100E+03 0.50210E+03
34 35 36 1 0.11100E+03 0.46020E+03
35 36 37 1 0.11100E+03 0.46020E+03
36 37 38 1 0.11100E+03 0.46020E+03
37 38 39 1 0.11100E+03 0.46020E+03
38 39 40 1 0.11100E+03 0.46020E+03
39 40 41 1 0.11100E+03 0.46020E+03
40 41 42 1 0.11100E+03 0.46020E+03
41 42 43 1 0.11100E+03 0.46020E+03
42 43 44 1 0.11100E+03 0.46020E+03
43 44 45 1 0.11100E+03 0.46020E+03
44 45 46 1 0.11100E+03 0.46020E+03
1 4 2 1 0.10950E+03 0.33470E+03
2 4 3 1 0.10950E+03 0.33470E+03
3 4 1 1 0.10950E+03 0.33470E+03
1 4 5 1 0.10950E+03 0.37660E+03
2 4 5 1 0.10950E+03 0.37660E+03
3 4 5 1 0.10950E+03 0.37660E+03
[ dihedrals ]
; ai aj ak al funct phi0 cp mult
1 4 5 6 1 0.0 3.76 3
4 5 6 7 1 0.0 5.85 3
5 6 7 8 1 0.0 3.76 3
6 7 8 11 1 0.0 1.05 3
6 7 8 11 1 0.0 3.14 2
7 8 11 12 1 0.0 1.05 3
7 8 11 12 1 0.0 3.14 2
8 11 12 13 1 0.0 3.76 3
11 12 13 14 1 0.0 2.09 2
11 12 13 30 1 0.0 5.85 3
11 12 13 30 1 0.0 0.42 2
12 13 30 31 1 0.0 5.85 3
12 13 30 31 1 0.0 0.42 2
12 13 14 15 1 0.0 3.77 3
13 30 31 32 1 0.0 3.76 3
13 14 15 17 1 180.0 16.74 2
14 13 30 31 1 0.0 2.09 2
14 15 17 18 1 0.0 0.42 6
15 17 18 19 1 0.0 5.86 3
17 18 19 20 3
18 19 20 21 3
19 20 21 22 3
20 21 22 23 3
21 22 23 24 3
22 23 24 25 3
; 23 24 25 26 1
24 25 26 27 3
25 26 27 28 3
26 27 28 29 3
13 30 31 32 1 0.0 3.76 3
30 31 32 34 1 180.0 16.74 2
31 32 34 35 1 0.0 0.42 6
32 34 35 36 1 0.0 5.86 3
34 35 36 37 3
35 36 37 38 3
36 37 38 39 3
37 38 39 40 3
38 39 40 41 3
39 40 41 42 3
40 41 42 43 3
41 42 43 44 3
42 43 44 45 3
43 44 45 46 3
[ dihedrals ]
; ai aj ak al funct
13 14 32 12 2 35.264 0.33470E+03
15 14 17 16 2 0.00000E+00 0.16740E+03
32 31 34 33 2 0.00000E+00 0.16740E+03
#ifdef POSRES_LIPID
#include "lipid_posre.itp"
#endif
------------------------------------------------------------------------
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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