<DIV>
<DIV>Hello,</DIV>
<DIV> </DIV>
<DIV>I am trying to draw the gromacs topology of C12E4 nonionic surfactant. I would like to simulate a C12E4 bilayer.</DIV>
<DIV>Its name is : tetraethyleneglycol monododecylether.</DIV>
<DIV>Its chemical formula is CH3-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-O-CH2-CH2-O-CH2-CH2-O-CH2-CH2-O-CH2-CH2-O-H</DIV>
<DIV> </DIV>
<DIV>I tried to draw the topology through the Dundee PRODRG2 Server, it gave me the following one (with a GROMACS topology quality on 0-10 scale: 6.7) :</DIV>
<DIV> </DIV>
<DIV>************************************************************************************************</DIV>
<DIV> </DIV>
<DIV>; <BR>; <BR>; This file was generated by PRODRG version 051017.0517<BR>; PRODRG written/copyrighted by Daan van Aalten<BR>; <BR>; Questions/comments to <A href="http://fr.f267.mail.yahoo.com/ym/Compose?To=dava@davapc1.bioch.dundee.ac.uk" target=_blank><FONT color=#003399>dava@davapc1.bioch.dundee.ac.uk</FONT></A><BR>; <BR>; When using this software in a publication, cite:<BR>; A. W. Schuettelkopf and D. M. F. van Aalten (2004).<BR>; PRODRG - a tool for high-throughput crystallography<BR>; of protein-ligand complexes.<BR>; Acta Crystallogr. D60,
1355--1363.<BR>; <BR>; </DIV>
<DIV>[ moleculetype ]<BR>; Name nrexcl<BR>DRG 3</DIV>
<DIV>[ atoms ]<BR>; nr type resnr resid atom cgnr charge mass<BR> 1 CH3 1 DRG CAA 1 -0.011 15.0350 <BR> 2 CH2 1 DRG CAC 1 0.003 14.0270 <BR> 3 CH2 1 DRG CAE 1 0.003 14.0270 <BR> 4 CH2 1 DRG CAF 1 0.002 14.0270
<BR> 5 CH2 1 DRG CAG 1 0.003 14.0270 <BR> 6 CH2 1 DRG CAH 2 0.000 14.0270 <BR> 7 CH2 1 DRG CAI 2 0.000 14.0270 <BR> 8 CH2 1 DRG CAJ 3 0.000 14.0270 <BR> 9 CH2 1 DRG
CAK 3 0.000 14.0270 <BR> 10 CH2 1 DRG CAL 4 0.001 14.0270 <BR> 11 CH2 1 DRG CAM 4 0.001 14.0270 <BR> 12 CS2 1 DRG CAO 4 0.082 14.0270 <BR> 13 OS 1 DRG OAW 4 -0.166 15.9994 <BR> 14 CS2
1 DRG CAQ 4 0.082 14.0270 <BR> 15 CS2 1 DRG CAS 5 0.082 14.0270 <BR> 16 OS 1 DRG OAY 5 -0.165 15.9994 <BR> 17 CS2 1 DRG CAU 5 0.083 14.0270 <BR> 18 CS2 1 DRG CAT 6 0.082 14.0270 <BR>
19 OS 1 DRG OAX 6 -0.165 15.9994 <BR> 20 CS2 1 DRG CAR 6 0.083 14.0270 <BR> 21 CS2 1 DRG CAP 7 0.082 14.0270 <BR> 22 OS 1 DRG OAV 7 -0.165 15.9994 <BR> 23 CS2 1 DRG CAN 7 0.083
14.0270 <BR> 24 CH2 1 DRG CAD 8 0.014 14.0270 <BR> 25 OA 1 DRG OAB 8 -0.013 15.9994 <BR> 26 HO 1 DRG HAA 8 -0.001 1.0080 </DIV>
<DIV>[ bonds ]<BR>; ai aj fu c0, c1, ...<BR> 1 2 1 0.153 334720.0 0.153 334720.0 ; CAA CAC <BR> 2 3 1 0.153 334720.0 0.153 334720.0 ; CAC CAE <BR> 3 4 1 0.153 334720.0 0.153 334720.0 ; CAE CAF <BR> 4 5 1 0.153 334720.0 0.153 334720.0 ; CAF CAG <BR> 5 6 1 0.153 334720.0 0.153 334720.0 ; CAG
CAH <BR> 6 7 1 0.153 334720.0 0.153 334720.0 ; CAH CAI <BR> 7 8 1 0.153 334720.0 0.153 334720.0 ; CAI CAJ <BR> 8 9 1 0.153 334720.0 0.153 334720.0 ; CAJ CAK <BR> 9 10 1 0.153 334720.0 0.153 334720.0 ; CAK CAL <BR> 10 11 1 0.153 334720.0 0.153 334720.0 ; CAL CAM <BR> 11 12
1 0.153 334720.0 0.153 334720.0 ; CAM CAO <BR> 12 13 1 0.144 251040.0 0.144 251040.0 ; CAO OAW <BR> 13 14 1 0.144 251040.0 0.144 251040.0 ; OAW CAQ <BR> 14 15 1 0.152 251040.0 0.152 251040.0 ; CAQ CAS <BR> 15 16 1 0.144 251040.0 0.144 251040.0 ; CAS OAY <BR> 16 17 1 0.144 251040.0 0.144
251040.0 ; OAY CAU <BR> 17 18 1 0.152 251040.0 0.152 251040.0 ; CAU CAT <BR> 18 19 1 0.144 251040.0 0.144 251040.0 ; CAT OAX <BR> 19 20 1 0.144 251040.0 0.144 251040.0 ; OAX CAR <BR> 20 21 1 0.152 251040.0 0.152 251040.0 ; CAR CAP <BR> 21 22 1 0.144 251040.0 0.144 251040.0 ; CAP OAV <BR> 22 23
1 0.144 251040.0 0.144 251040.0 ; OAV CAN <BR> 23 24 1 0.153 334720.0 0.153 334720.0 ; CAN CAD <BR> 24 25 1 0.143 334720.0 0.143 334720.0 ; CAD OAB <BR> 25 26 1 0.100 313800.0 0.100 313800.0 ; OAB HAA </DIV>
<DIV>[ pairs ]<BR>; ai aj fu c0, c1, ...<BR> 1 4 1 ; CAA CAF <BR> 2 5 1 ; CAC CAG <BR> 3 6
1 ; CAE CAH <BR> 4 7 1 ; CAF CAI <BR> 5 8 1 ; CAG CAJ <BR>
6 9 1 ; CAH CAK <BR> 7 10 1 ; CAI CAL <BR> 8 11 1 ; CAJ CAM
<BR> 9 12 1 ; CAK CAO <BR> 10 13 1 ; CAL OAW <BR> 11 14 1 ; CAM CAQ
<BR> 12 15 1 ; CAO CAS <BR> 13 16 1 ; OAW OAY <BR> 14 17 1 ; CAQ CAU <BR>
15 18 1 ; CAS CAT <BR> 16 19 1 ; OAY OAX <BR> 17 20 1 ; CAU CAR <BR> 18
21 1 ; CAT CAP <BR> 19 22 1 ; OAX OAV <BR> 20 23 1 ; CAR CAN <BR> 21
24 1 ; CAP CAD <BR> 22 25 1 ; OAV OAB <BR> 23 26 1 ; CAN HAA </DIV>
<DIV>[ angles ]<BR>; ai aj ak fu c0, c1, ...<BR> 1 2 3 1 111.0 460.2 111.0 460.2 ; CAA CAC CAE <BR> 2 3 4 1 111.0 460.2 111.0 460.2 ; CAC CAE CAF <BR> 3 4 5 1 111.0 460.2 111.0 460.2 ; CAE CAF CAG <BR> 4 5 6 1 111.0 460.2 111.0
460.2 ; CAF CAG CAH <BR> 5 6 7 1 111.0 460.2 111.0 460.2 ; CAG CAH CAI <BR> 6 7 8 1 111.0 460.2 111.0 460.2 ; CAH CAI CAJ <BR> 7 8 9 1 111.0 460.2 111.0 460.2 ; CAI CAJ CAK <BR> 8 9 10 1 111.0 460.2 111.0 460.2 ; CAJ
CAK CAL <BR> 9 10 11 1 111.0 460.2 111.0 460.2 ; CAK CAL CAM <BR> 10 11 12 1 111.0 460.2 111.0 460.2 ; CAL CAM CAO <BR> 11 12 13 1 109.5 284.5 109.5 284.5 ; CAM CAO OAW <BR> 12 13 14 1 109.5 334.7 109.5 334.7 ; CAO OAW CAQ <BR> 13 14 15
1 109.5 284.5 109.5 284.5 ; OAW CAQ CAS <BR> 14 15 16 1 109.5 284.5 109.5 284.5 ; CAQ CAS OAY <BR> 15 16 17 1 109.5 334.7 109.5 334.7 ; CAS OAY CAU <BR> 16 17 18 1 109.5 284.5 109.5 284.5 ; OAY CAU CAT <BR> 17 18 19 1 109.5 284.5
109.5 284.5 ; CAU CAT OAX <BR> 18 19 20 1 109.5 334.7 109.5 334.7 ; CAT OAX CAR <BR> 19 20 21 1 109.5 284.5 109.5 284.5 ; OAX CAR CAP <BR> 20 21 22 1 109.5 284.5 109.5 284.5 ; CAR CAP OAV <BR> 21 22 23 1 109.5 334.7 109.5 334.7 ; CAP OAV
CAN <BR> 22 23 24 1 109.5 284.5 109.5 284.5 ; OAV CAN CAD <BR> 23 24 25 1 109.5 460.2 109.5 460.2 ; CAN CAD OAB <BR> 24 25 26 1 109.5 397.5 109.5 397.5 ; CAD OAB HAA </DIV>
<DIV>[ dihedrals ]<BR>; ai aj ak al fu c0, c1, m, ...<BR> 4 3 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih CAF CAE CAC CAA <BR> 5 4 3 2 1 0.0 5.9 3 0.0 5.9 3 ; dih CAG CAF CAE CAC <BR> 6 5 4 3 1 0.0 5.9 3 0.0 5.9 3 ; dih CAH CAG CAF CAE <BR> 7 6 5 4 1 0.0 5.9
3 0.0 5.9 3 ; dih CAI CAH CAG CAF <BR> 8 7 6 5 1 0.0 5.9 3 0.0 5.9 3 ; dih CAJ CAI CAH CAG <BR> 9 8 7 6 1 0.0 5.9 3 0.0 5.9 3 ; dih CAK CAJ CAI CAH <BR> 10 9 8 7 1 0.0 5.9 3 0.0 5.9 3 ; dih CAL CAK CAJ CAI <BR> 11 10 9 8 1
0.0 5.9 3 0.0 5.9 3 ; dih CAM CAL CAK CAJ <BR> 12 11 10 9 1 0.0 5.9 3 0.0 5.9 3 ; dih CAO CAM CAL CAK <BR> 10 11 12 13 1 0.0 5.9 3 0.0 5.9 3 ; dih CAL CAM CAO OAW <BR> 11 12 13 14 1 0.0 3.8 3 0.0 3.8 3 ; dih CAM CAO OAW CAQ <BR> 15 14 13 12 1 0.0 3.8
3 0.0 3.8 3 ; dih CAS CAQ OAW CAO <BR> 13 14 15 16 1 0.0 5.9 3 0.0 5.9 3 ; dih OAW CAQ CAS OAY <BR> 14 15 16 17 1 0.0 3.8 3 0.0 3.8 3 ; dih CAQ CAS OAY CAU <BR> 18 17 16 15 1 0.0 3.8 3 0.0 3.8 3 ; dih CAT CAU OAY CAS <BR> 16 17 18 19 1 0.0 5.9 3 0.0 5.9
3 ; dih OAY CAU CAT OAX <BR> 17 18 19 20 1 0.0 3.8 3 0.0 3.8 3 ; dih CAU CAT OAX CAR <BR> 21 20 19 18 1 0.0 3.8 3 0.0 3.8 3 ; dih CAP CAR OAX CAT <BR> 19 20 21 22 1 0.0 5.9 3 0.0 5.9 3 ; dih OAX CAR CAP OAV <BR> 20 21 22 23 1 0.0 3.8 3 0.0 3.8 3 ; dih CAR CAP OAV
CAN <BR> 24 23 22 21 1 0.0 3.8 3 0.0 3.8 3 ; dih CAD CAN OAV CAP <BR> 22 23 24 25 1 0.0 5.9 3 0.0 5.9 3 ; dih OAV CAN CAD OAB <BR> 23 24 25 26 1 0.0 1.3 3 0.0 1.3 3 ; dih CAN CAD OAB HAA </DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV>**********************************************************************************************</DIV>
<DIV> </DIV>
<DIV>The topology provided here seems to have a low topology quality.</DIV>
<DIV>It will be possible to build the topology for C12E4 from the topology of an ether-oxyd, and not a lipid.</DIV>
<DIV> </DIV>
<DIV>Has someone ever build a topology of an ether-oxyd ?</DIV>
<DIV> </DIV>
<DIV>Thank you very much.</DIV>
<DIV> </DIV>
<DIV>Erol</DIV></DIV><p>
                <hr size=1>
<b><font color=#FF0000>Appel audio GRATUIT</font> partout dans le monde</b> avec le nouveau Yahoo! Messenger<br>
<a href="http://us.rd.yahoo.com/messenger/mail_taglines/default/*http://fr.messenger.yahoo.com">Téléchargez le ici !</a>