; DPPC itp file
; Use ffG43A1-S3 parameter files
; 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 <jalem...@vt.edu> wrote:
>
>
> sahajmo...@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" <jalem...@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 | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> ========================================
>>> _______________________________________________
>>> gmx-users mailing list gmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
>>> posting!
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-requ...@gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>
>>
> --
> ========================================
>
> 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
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
--
MOHIT KUMAR
Molecular Biochemistry & Biophysics
Graduate Student
Illinois Institute of Technology
Chicago,IL, USA
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