[gmx-users] pairing error
Justin A. Lemkul
jalemkul at vt.edu
Tue Aug 11 20:24:18 CEST 2009
mohit kumar wrote:
> ; DPPC itp file
> ; Use ffG43A1-S3 parameter files
There's nothing obviously wrong with this topology. Are you using your own
modified version of ffG43a1? If so, the problem may lie in the [ pairtypes ]
directive in the force field file, not this .itp file.
-Justin
> ; KW-type potential (gd_kw20) is used for the dihedrals -CH2-CH2-CH2-CH2-
> ; of the hydrocarbon chains.
> ; gd_kw5 for -OA-C(carbonyl)-CH2-CH2- in Sn2 and Sn2 chains
> ; gd_kw7 for -C(carbonyl)-CH2-CH2-CH2-
> ; Partial charges on the head group atoms were derived from HF/6-31G*
> ; calculation
> ; For use with PME method only
> ;
> [ moleculetype ]
> ; Name nrexcl
> POPC 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> typeB chargeB massB
> 1 CH3* 1 POPC C1 1 0.4 15.035
> 2 CH3* 1 POPC C2 2 0.4 15.035
> 3 CH3* 1 POPC C3 3 0.4 15.035
> 4 NL 1 POPC N4 4 -0.5 14.0067
> 5 CH2* 1 POPC C5 5 0.3 14.027
> 6 CH2* 1 POPC C6 6 0.4 14.027
> 7 OA 1 POPC OS7 7 -0.8 15.9994
> 8 P 1 POPC P8 8 1.7 30.9738
> 9 OM* 1 POPC OM9 9 -0.8 15.9994
> 10 OM* 1 POPC OM10 10 -0.8 15.9994
> 11 OA 1 POPC OS11 11 -0.7 15.9994
> 12 CH2* 1 POPC C12 12 0.4 14.027
> 13 CH1* 1 POPC C13 13 0.3 13.019
> 14 OA 1 POPC OS14 14 -0.7 15.9994
> 15 CO* 1 POPC C15 15 0.7 12.011
> 16 O* 1 POPC O16 16 -0.7 15.9994
> 17 CH2* 1 POPC C17 17 0 14.027
> 18 CH2* 1 POPC C18 17 0 14.027
> 19 CH2* 1 POPC C19 17 0 14.027
> 20 CH2* 1 POPC C20 18 0 14.027
> 21 CH2* 1 POPC C21 18 0 14.027
> 22 CH2* 1 POPC C22 18 0 14.027
> 23 CH2* 1 POPC C23 19 0 14.027
> 24 C*H1 1 POPC C24 19 0 13.019
> 25 C*H1 1 POPC C25 19 0 13.019
> 26 CH2* 1 POPC C26 20 0 14.027
> 27 CH2* 1 POPC C27 20 0 14.027
> 28 CH2* 1 POPC C28 20 0 14.027
> 29 CH2* 1 POPC C29 21 0 14.027
> 30 CH2* 1 POPC C30 21 0 14.027
> 31 CH2* 1 POPC C31 21 0 15.035
> 32 CH2* 1 POPC C32 22 0 14.027
> 33 CH3* 1 POPC C33 22 0.0 15.035
> 34 CH2* 1 POPC C34 23 0.5 14.027
> 35 OA 1 POPC OS35 24 -0.7 15.9994
> 36 CO* 1 POPC C36 25 0.8 12.011
> 37 O* 1 POPC O37 26 -0.6 15.9994
> 38 CH2* 1 POPC C38 27 0 14.027
> 39 CH2* 1 POPC C39 27 0 14.027
> 40 CH2* 1 POPC C40 27 0 14.027
> 41 CH2* 1 POPC C41 28 0 14.027
> 42 CH2* 1 POPC C42 28 0 14.027
> 43 CH2* 1 POPC C43 28 0 14.027
> 44 CH2* 1 POPC C44 29 0 14.027
> 45 CH2* 1 POPC C45 29 0 13.019
> 46 CH2* 1 POPC C46 29 0 13.019
> 47 CH2* 1 POPC C47 30 0 14.027
> 48 CH2* 1 POPC C48 30 0 14.027
> 49 CH2* 1 POPC C49 30 0 14.027
> 50 CH2* 1 POPC C50 31 0 14.027
> 51 CH2* 1 POPC C51 31 0 14.027
> 52 CH3* 1 POPC C52 31 0 15.035
>
> [ bonds ]
> ; ai aj funct c0 c1 c2 c3
> 1 4 2 gb_20
> 2 4 2 gb_20
> 3 4 2 gb_20
> 4 5 2 gb_20
> 5 6 2 gb_26
> 6 7 2 gb_17
> 7 8 2 gb_27
> 8 9 2 gb_23
> 8 10 2 gb_23
> 8 11 2 gb_27
> 11 12 2 gb_17
> 12 13 2 gb_26
> 13 14 2 gb_17
> 13 34 2 gb_26
> 14 15 2 gb_12
> 15 16 2 gb_4
> 15 17 2 gb_58b ; gb_24
> 17 18 2 gb_26
> 18 19 2 gb_26
> 19 20 2 gb_26
> 20 21 2 gb_26
> 21 22 2 gb_26
> 22 23 2 gb_26
> 23 24 2 gb_58
> 24 25 2 gb_57
> 25 26 2 gb_58
> 26 27 2 gb_26
> 27 28 2 gb_26
> 28 29 2 gb_26
> 29 30 2 gb_26
> 30 31 2 gb_26
> 31 32 2 gb_26
> 32 33 2 gb_26
> 34 35 2 gb_17
> 35 36 2 gb_12
> 36 37 2 gb_4
> 36 38 2 gb_58b ; gb_24
> 38 39 2 gb_26
> 39 40 2 gb_26
> 40 41 2 gb_26
> 41 42 2 gb_26
> 42 43 2 gb_26
> 43 44 2 gb_26
> 44 45 2 gb_26
> 45 46 2 gb_26
> 46 47 2 gb_26
> 47 48 2 gb_26
> 48 49 2 gb_26
> 49 50 2 gb_26
> 50 51 2 gb_26
> 51 52 2 gb_26
>
> [ pairs ]
> ; ai aj funct c0 c1 c2 c3
> 1 6 1
> 2 6 1
> 3 6 1
> 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 34 1
> 12 15 1
> 12 35 1
> ; 13 16 1 ; gd_kw32
> ; 13 17 1 ; gd_kw32
> 13 36 1
> ; 14 18 1 ; gd_kw5
> 14 35 1
> ; 15 19 1 ; gd_kw7
> 15 34 1
> ; 16 18 1 ; gd_kw5
> ; 21 24 1 ; gd_kw4a1
> ; 22 25 1 ;gd_kw34a1
> 23 26 1
> ; 24 27 1 ; gd_kw34a1
> ; 25 28 1 ;gd_kw4a1
> ; 34 37 1 ; gd_kw32
> ; 34 38 1 ; gd_kw32
> ; 35 39 1 ; gd_kw5
> ; 36 40 1 ; gd_kw7
> ; 37 39 1 ; gd_kw5
>
> [ angles ]
> ; ai aj ak funct c0 c1
> c2 c3
> 1 4 2 2 ga_12
> 1 4 3 2 ga_12
> 1 4 5 2 ga_12
> 2 4 3 2 ga_12
> 2 4 5 2 ga_12
> 3 4 5 2 ga_12
> 4 5 6 2 ga_14
> 5 6 7 2 ga_14
> 6 7 8 2 ga_25
> 7 8 9 2 ga_13
> 7 8 10 2 ga_13
> 7 8 11 2 ga_4
> 9 8 10 2 ga_28
> 9 8 11 2 ga_13
> 10 8 11 2 ga_13
> 8 11 12 2 ga_25
> 11 12 13 2 ga_14
> 12 13 14 2 ga_12
> 12 13 34 2 ga_12
> 14 13 34 2 ga_12
> 13 14 15 2 ga_18
> 14 15 16 2 ga_32
> 14 15 17 2 ga_14
> 16 15 17 2 ga_34
> 15 17 18 2 ga_14
> 17 18 19 2 ga_14
> 18 19 20 2 ga_14
> 19 20 21 2 ga_14
> 20 21 22 2 ga_14
> 21 22 23 2 ga_14
> 22 23 24 2 ga_49
> 23 24 25 2 ga_47
> 24 25 26 2 ga_47
> 25 26 27 2 ga_49
> 26 27 28 2 ga_14
> 27 28 29 2 ga_14
> 28 29 30 2 ga_14
> 29 30 31 2 ga_14
> 30 31 32 2 ga_14
> 31 32 33 2 ga_14
> 13 34 35 2 ga_14
> 34 35 36 2 ga_18
> 35 36 37 2 ga_32
> 35 36 38 2 ga_14
> 36 38 39 2 ga_14
> 37 36 38 2 ga_34
> 38 39 40 2 ga_14
> 39 40 41 2 ga_14
> 40 41 42 2 ga_14
> 41 42 43 2 ga_14
> 42 43 44 2 ga_14
> 43 44 45 2 ga_14
> 44 45 46 2 ga_14
> 45 46 47 2 ga_14
> 46 47 48 2 ga_14
> 47 48 49 2 ga_14
> 48 49 50 2 ga_14
> 49 50 51 2 ga_14
> 50 51 52 2 ga_14
>
> [ dihedrals ]
> ; ai aj ak al funct c0 c1
> c2 c3 c4 c5
> 3 4 5 6 1 gd_17d ;gd_kw36
> 4 5 6 7 3 gd_swc6n
> 5 6 7 8 1 gd_14
> 6 7 8 11 3 gd_s0911
> 7 8 11 12 3 gd_s0911
> 8 11 12 13 1 gd_14
> 11 12 13 34 1 gd_17
> 12 13 14 15 3 gd_swc1 ; sn2 chain
> 12 13 34 35 1 gd_17
> 13 14 15 17 3 gd_kw32
> 14 15 17 18 3 gd_kw5
> 15 17 18 19 3 gd_kw7
> 17 18 19 20 3 gd_kw20
> 18 19 20 21 3 gd_kw20
> 19 20 21 22 3 gd_kw20
> 20 21 22 23 3 gd_kw20
> 21 22 23 24 3 gd_kw4a1
> 22 23 24 25 3 gd_kw34a1
> 23 24 25 26 1 gd_5b
> 24 25 26 27 3 gd_kw34a1
> 25 26 27 28 3 gd_kw4a1
> 26 27 28 29 3 gd_kw20
> 27 28 29 30 3 gd_kw20
> 28 29 30 31 3 gd_kw20
> 29 30 31 32 3 gd_kw20
> 30 31 32 33 3 gd_kw20
> 13 34 35 36 3 gd_swc1a
> 34 35 36 38 3 gd_kw32
> 35 36 38 39 3 gd_kw5
> 36 38 39 40 3 gd_kw7
> 38 39 40 41 3 gd_kw20
> 39 40 41 42 3 gd_kw20
> 40 41 42 43 3 gd_kw20
> 41 42 43 44 3 gd_kw20
> 42 43 44 45 3 gd_kw20
> 43 44 45 46 3 gd_kw20
> 44 45 46 47 3 gd_kw20
> 45 46 47 48 3 gd_kw20
> 46 47 48 49 3 gd_kw20
> 47 48 49 50 3 gd_kw20
> 48 49 50 51 3 gd_kw20
> 49 50 51 52 3 gd_kw20
>
> [ dihedrals ]
> ; ai aj ak al funct c0 c1
> c2 c3
> 13 14 34 12 2 gi_2
> 15 14 17 16 2 gi_1
> 36 35 38 37 2 gi_1
>
>
> On Mon, Aug 10, 2009 at 2:13 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> sahajmohit at gmail.com <mailto:sahajmohit at gmail.com> wrote:
>
> So wat shud I do now I send u the attach files
>
>
> Copy and paste the problematic section from your topology into an
> email so we can all see it.
>
> -Justin
>
>
>
> Regards,
> Mohit Kumar
>
> On 10-Aug-2009, at 12:05 PM, "Justin A. Lemkul" <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> mohit kumar wrote:
>
> im using dell core 2 duo with linux mint
>
>
> OK, so what about showing us the topology? That's probably
> a lot more relevant, anyway.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
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>
>
>
> --
> MOHIT KUMAR
> Molecular Biochemistry & Biophysics
> Graduate Student
> Illinois Institute of Technology
> Chicago,IL, USA
>
--
========================================
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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