[gmx-users] Which membrane result is more reliable?
Justin A. Lemkul
jalemkul at vt.edu
Sun Oct 25 22:18:44 CET 2009
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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>
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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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