; DPPC itp file<br>; Use ffG43A1-S3 parameter files<br>; KW-type potential (gd_kw20) is used for the dihedrals -CH2-CH2-CH2-CH2-<br>; of the hydrocarbon chains.<br>; gd_kw5 for -OA-C(carbonyl)-CH2-CH2- in Sn2 and Sn2 chains<br>
; gd_kw7 for -C(carbonyl)-CH2-CH2-CH2-<br>; Partial charges on the head group atoms were derived from HF/6-31G*<br>; calculation<br>; For use with PME method only<br>;<br>[ moleculetype ]<br>; Name nrexcl<br>
POPC 3<br><br>[ atoms ]<br>; nr type resnr residue atom cgnr charge mass typeB chargeB massB<br> 1 CH3* 1 POPC C1 1 0.4 15.035 <br> 2 CH3* 1 POPC C2 2 0.4 15.035 <br>
3 CH3* 1 POPC C3 3 0.4 15.035 <br> 4 NL 1 POPC N4 4 -0.5 14.0067 <br> 5 CH2* 1 POPC C5 5 0.3 14.027 <br> 6 CH2* 1 POPC C6 6 0.4 14.027 <br>
7 OA 1 POPC OS7 7 -0.8 15.9994 <br> 8 P 1 POPC P8 8 1.7 30.9738 <br> 9 OM* 1 POPC OM9 9 -0.8 15.9994 <br> 10 OM* 1 POPC OM10 10 -0.8 15.9994 <br>
11 OA 1 POPC OS11 11 -0.7 15.9994 <br> 12 CH2* 1 POPC C12 12 0.4 14.027 <br> 13 CH1* 1 POPC C13 13 0.3 13.019 <br> 14 OA 1 POPC OS14 14 -0.7 15.9994 <br>
15 CO* 1 POPC C15 15 0.7 12.011 <br> 16 O* 1 POPC O16 16 -0.7 15.9994 <br> 17 CH2* 1 POPC C17 17 0 14.027 <br> 18 CH2* 1 POPC C18 17 0 14.027 <br>
19 CH2* 1 POPC C19 17 0 14.027 <br> 20 CH2* 1 POPC C20 18 0 14.027 <br> 21 CH2* 1 POPC C21 18 0 14.027 <br> 22 CH2* 1 POPC C22 18 0 14.027 <br>
23 CH2* 1 POPC C23 19 0 14.027 <br> 24 C*H1 1 POPC C24 19 0 13.019 <br> 25 C*H1 1 POPC C25 19 0 13.019 <br> 26 CH2* 1 POPC C26 20 0 14.027 <br>
27 CH2* 1 POPC C27 20 0 14.027 <br> 28 CH2* 1 POPC C28 20 0 14.027<br> 29 CH2* 1 POPC C29 21 0 14.027 <br> 30 CH2* 1 POPC C30 21 0 14.027 <br>
31 CH2* 1 POPC C31 21 0 15.035 <br> 32 CH2* 1 POPC C32 22 0 14.027 <br> 33 CH3* 1 POPC C33 22 0.0 15.035 <br> 34 CH2* 1 POPC C34 23 0.5 14.027 <br>
35 OA 1 POPC OS35 24 -0.7 15.9994 <br> 36 CO* 1 POPC C36 25 0.8 12.011 <br> 37 O* 1 POPC O37 26 -0.6 15.9994 <br> 38 CH2* 1 POPC C38 27 0 14.027 <br>
39 CH2* 1 POPC C39 27 0 14.027 <br> 40 CH2* 1 POPC C40 27 0 14.027 <br> 41 CH2* 1 POPC C41 28 0 14.027 <br> 42 CH2* 1 POPC C42 28 0 14.027 <br>
43 CH2* 1 POPC C43 28 0 14.027 <br> 44 CH2* 1 POPC C44 29 0 14.027 <br> 45 CH2* 1 POPC C45 29 0 13.019 <br> 46 CH2* 1 POPC C46 29 0 13.019 <br>
47 CH2* 1 POPC C47 30 0 14.027 <br> 48 CH2* 1 POPC C48 30 0 14.027 <br> 49 CH2* 1 POPC C49 30 0 14.027<br> 50 CH2* 1 POPC C50 31 0 14.027 <br>
51 CH2* 1 POPC C51 31 0 14.027 <br> 52 CH3* 1 POPC C52 31 0 15.035 <br><br>[ bonds ]<br>; ai aj funct c0 c1 c2 c3<br>
1 4 2 gb_20<br> 2 4 2 gb_20<br> 3 4 2 gb_20<br> 4 5 2 gb_20<br> 5 6 2 gb_26<br> 6 7 2 gb_17<br> 7 8 2 gb_27<br> 8 9 2 gb_23<br>
8 10 2 gb_23<br> 8 11 2 gb_27<br> 11 12 2 gb_17<br> 12 13 2 gb_26<br> 13 14 2 gb_17<br> 13 34 2 gb_26<br> 14 15 2 gb_12<br> 15 16 2 gb_4<br>
15 17 2 gb_58b ; gb_24<br> 17 18 2 gb_26<br> 18 19 2 gb_26<br> 19 20 2 gb_26<br> 20 21 2 gb_26<br> 21 22 2 gb_26<br> 22 23 2 gb_26<br> 23 24 2 gb_58<br>
24 25 2 gb_57<br> 25 26 2 gb_58<br> 26 27 2 gb_26<br> 27 28 2 gb_26<br> 28 29 2 gb_26<br> 29 30 2 gb_26<br> 30 31 2 gb_26<br> 31 32 2 gb_26<br>
32 33 2 gb_26<br> 34 35 2 gb_17<br> 35 36 2 gb_12<br> 36 37 2 gb_4<br> 36 38 2 gb_58b ; gb_24<br> 38 39 2 gb_26<br> 39 40 2 gb_26<br> 40 41 2 gb_26<br>
41 42 2 gb_26<br> 42 43 2 gb_26<br> 43 44 2 gb_26<br> 44 45 2 gb_26<br> 45 46 2 gb_26<br> 46 47 2 gb_26<br> 47 48 2 gb_26<br> 48 49 2 gb_26<br>
49 50 2 gb_26<br> 50 51 2 gb_26<br> 51 52 2 gb_26<br><br>[ pairs ]<br>; ai aj funct c0 c1 c2 c3<br> 1 6 1 <br> 2 6 1 <br>
3 6 1 <br> 4 7 1 <br> 5 8 1 <br> 6 9 1 <br> 6 10 1 <br> 6 11 1 <br> 7 12 1 <br> 8 13 1 <br> 9 12 1 <br> 10 12 1 <br> 11 14 1 <br>
11 34 1 <br> 12 15 1 <br> 12 35 1 <br>; 13 16 1 ; gd_kw32<br>; 13 17 1 ; gd_kw32<br> 13 36 1 <br>; 14 18 1 ; gd_kw5<br> 14 35 1 <br>; 15 19 1 ; gd_kw7<br>
15 34 1 <br>; 16 18 1 ; gd_kw5<br>; 21 24 1 ; gd_kw4a1<br>; 22 25 1 ;gd_kw34a1<br> 23 26 1<br>; 24 27 1 ; gd_kw34a1<br>; 25 28 1 ;gd_kw4a1<br>; 34 37 1 ; gd_kw32 <br>
; 34 38 1 ; gd_kw32 <br>; 35 39 1 ; gd_kw5<br>; 36 40 1 ; gd_kw7<br>; 37 39 1 ; gd_kw5<br><br>[ angles ]<br>; ai aj ak funct c0 c1 c2 c3<br>
1 4 2 2 ga_12<br> 1 4 3 2 ga_12<br> 1 4 5 2 ga_12<br> 2 4 3 2 ga_12<br> 2 4 5 2 ga_12<br> 3 4 5 2 ga_12<br> 4 5 6 2 ga_14<br>
5 6 7 2 ga_14<br> 6 7 8 2 ga_25<br> 7 8 9 2 ga_13<br> 7 8 10 2 ga_13<br> 7 8 11 2 ga_4<br> 9 8 10 2 ga_28<br> 9 8 11 2 ga_13<br>
10 8 11 2 ga_13<br> 8 11 12 2 ga_25<br> 11 12 13 2 ga_14<br> 12 13 14 2 ga_12<br> 12 13 34 2 ga_12<br> 14 13 34 2 ga_12<br> 13 14 15 2 ga_18 <br>
14 15 16 2 ga_32<br> 14 15 17 2 ga_14<br> 16 15 17 2 ga_34<br> 15 17 18 2 ga_14<br> 17 18 19 2 ga_14<br> 18 19 20 2 ga_14<br> 19 20 21 2 ga_14<br>
20 21 22 2 ga_14<br> 21 22 23 2 ga_14<br> 22 23 24 2 ga_49<br> 23 24 25 2 ga_47<br> 24 25 26 2 ga_47<br> 25 26 27 2 ga_49<br> 26 27 28 2 ga_14<br>
27 28 29 2 ga_14<br> 28 29 30 2 ga_14<br> 29 30 31 2 ga_14<br> 30 31 32 2 ga_14<br> 31 32 33 2 ga_14<br> 13 34 35 2 ga_14<br> 34 35 36 2 ga_18 <br>
35 36 37 2 ga_32<br> 35 36 38 2 ga_14<br> 36 38 39 2 ga_14<br> 37 36 38 2 ga_34<br> 38 39 40 2 ga_14<br> 39 40 41 2 ga_14<br> 40 41 42 2 ga_14<br>
41 42 43 2 ga_14<br> 42 43 44 2 ga_14<br> 43 44 45 2 ga_14<br> 44 45 46 2 ga_14<br> 45 46 47 2 ga_14<br> 46 47 48 2 ga_14<br> 47 48 49 2 ga_14<br>
48 49 50 2 ga_14<br> 49 50 51 2 ga_14<br> 50 51 52 2 ga_14<br><br>[ dihedrals ]<br>; ai aj ak al funct c0 c1 c2 c3 c4 c5<br>
3 4 5 6 1 gd_17d ;gd_kw36 <br> 4 5 6 7 3 gd_swc6n <br> 5 6 7 8 1 gd_14<br> 6 7 8 11 3 gd_s0911<br> 7 8 11 12 3 gd_s0911<br>
8 11 12 13 1 gd_14<br> 11 12 13 34 1 gd_17 <br> 12 13 14 15 3 gd_swc1 ; sn2 chain <br> 12 13 34 35 1 gd_17<br> 13 14 15 17 3 gd_kw32 <br>
14 15 17 18 3 gd_kw5 <br> 15 17 18 19 3 gd_kw7<br> 17 18 19 20 3 gd_kw20<br> 18 19 20 21 3 gd_kw20<br> 19 20 21 22 3 gd_kw20<br> 20 21 22 23 3 gd_kw20<br>
21 22 23 24 3 gd_kw4a1 <br> 22 23 24 25 3 gd_kw34a1 <br> 23 24 25 26 1 gd_5b<br> 24 25 26 27 3 gd_kw34a1 <br> 25 26 27 28 3 gd_kw4a1 <br>
26 27 28 29 3 gd_kw20<br> 27 28 29 30 3 gd_kw20<br> 28 29 30 31 3 gd_kw20<br> 29 30 31 32 3 gd_kw20<br> 30 31 32 33 3 gd_kw20<br> 13 34 35 36 3 gd_swc1a <br>
34 35 36 38 3 gd_kw32 <br> 35 36 38 39 3 gd_kw5 <br> 36 38 39 40 3 gd_kw7<br> 38 39 40 41 3 gd_kw20<br> 39 40 41 42 3 gd_kw20<br>
40 41 42 43 3 gd_kw20<br> 41 42 43 44 3 gd_kw20<br> 42 43 44 45 3 gd_kw20 <br> 43 44 45 46 3 gd_kw20 <br> 44 45 46 47 3 gd_kw20<br>
45 46 47 48 3 gd_kw20 <br> 46 47 48 49 3 gd_kw20 <br> 47 48 49 50 3 gd_kw20<br> 48 49 50 51 3 gd_kw20<br> 49 50 51 52 3 gd_kw20<br>
<br>[ dihedrals ]<br>; ai aj ak al funct c0 c1 c2 c3<br> 13 14 34 12 2 gi_2<br> 15 14 17 16 2 gi_1<br> 36 35 38 37 2 gi_1<br>
<br><br><div class="gmail_quote">On Mon, Aug 10, 2009 at 2:13 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
<a href="mailto:sahajmohit@gmail.com" target="_blank">sahajmohit@gmail.com</a> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
So wat shud I do now I send u the attach files<br>
<br>
</blockquote>
<br></div>
Copy and paste the problematic section from your topology into an email so we can all see it.<br><font color="#888888">
<br>
-Justin</font><div><div></div><div class="h5"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Regards,<br>
Mohit Kumar<br>
<br>
On 10-Aug-2009, at 12:05 PM, "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>> wrote:<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
<br>
mohit kumar wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
im using dell core 2 duo with linux mint<br>
</blockquote>
<br>
OK, so what about showing us the topology? That's probably a lot more relevant, anyway.<br>
<br>
-Justin<br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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</blockquote>
<br>
</blockquote>
<br></div></div>
-- <br><div><div></div><div class="h5">
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>MOHIT KUMAR<br>Molecular Biochemistry & Biophysics<br>Graduate Student<br>Illinois Institute of Technology<br>Chicago,IL, USA<br><br>