[gmx-users] C12E4 nonionic surfactant topology
Erol Kurtisovski
erol_kurtisovski2 at yahoo.fr
Mon Nov 7 12:02:10 CET 2005
Hello,
I am trying to draw the gromacs topology of C12E4 nonionic surfactant. I would like to simulate a C12E4 bilayer.
Its name is : tetraethyleneglycol monododecylether.
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
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) :
************************************************************************************************
;
;
; This file was generated by PRODRG version 051017.0517
; PRODRG written/copyrighted by Daan van Aalten
;
; Questions/comments to dava at davapc1.bioch.dundee.ac.uk
;
; When using this software in a publication, cite:
; A. W. Schuettelkopf and D. M. F. van Aalten (2004).
; PRODRG - a tool for high-throughput crystallography
; of protein-ligand complexes.
; Acta Crystallogr. D60, 1355--1363.
;
;
[ moleculetype ]
; Name nrexcl
DRG 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 CH3 1 DRG CAA 1 -0.011 15.0350
2 CH2 1 DRG CAC 1 0.003 14.0270
3 CH2 1 DRG CAE 1 0.003 14.0270
4 CH2 1 DRG CAF 1 0.002 14.0270
5 CH2 1 DRG CAG 1 0.003 14.0270
6 CH2 1 DRG CAH 2 0.000 14.0270
7 CH2 1 DRG CAI 2 0.000 14.0270
8 CH2 1 DRG CAJ 3 0.000 14.0270
9 CH2 1 DRG CAK 3 0.000 14.0270
10 CH2 1 DRG CAL 4 0.001 14.0270
11 CH2 1 DRG CAM 4 0.001 14.0270
12 CS2 1 DRG CAO 4 0.082 14.0270
13 OS 1 DRG OAW 4 -0.166 15.9994
14 CS2 1 DRG CAQ 4 0.082 14.0270
15 CS2 1 DRG CAS 5 0.082 14.0270
16 OS 1 DRG OAY 5 -0.165 15.9994
17 CS2 1 DRG CAU 5 0.083 14.0270
18 CS2 1 DRG CAT 6 0.082 14.0270
19 OS 1 DRG OAX 6 -0.165 15.9994
20 CS2 1 DRG CAR 6 0.083 14.0270
21 CS2 1 DRG CAP 7 0.082 14.0270
22 OS 1 DRG OAV 7 -0.165 15.9994
23 CS2 1 DRG CAN 7 0.083 14.0270
24 CH2 1 DRG CAD 8 0.014 14.0270
25 OA 1 DRG OAB 8 -0.013 15.9994
26 HO 1 DRG HAA 8 -0.001 1.0080
[ bonds ]
; ai aj fu c0, c1, ...
1 2 1 0.153 334720.0 0.153 334720.0 ; CAA CAC
2 3 1 0.153 334720.0 0.153 334720.0 ; CAC CAE
3 4 1 0.153 334720.0 0.153 334720.0 ; CAE CAF
4 5 1 0.153 334720.0 0.153 334720.0 ; CAF CAG
5 6 1 0.153 334720.0 0.153 334720.0 ; CAG CAH
6 7 1 0.153 334720.0 0.153 334720.0 ; CAH CAI
7 8 1 0.153 334720.0 0.153 334720.0 ; CAI CAJ
8 9 1 0.153 334720.0 0.153 334720.0 ; CAJ CAK
9 10 1 0.153 334720.0 0.153 334720.0 ; CAK CAL
10 11 1 0.153 334720.0 0.153 334720.0 ; CAL CAM
11 12 1 0.153 334720.0 0.153 334720.0 ; CAM CAO
12 13 1 0.144 251040.0 0.144 251040.0 ; CAO OAW
13 14 1 0.144 251040.0 0.144 251040.0 ; OAW CAQ
14 15 1 0.152 251040.0 0.152 251040.0 ; CAQ CAS
15 16 1 0.144 251040.0 0.144 251040.0 ; CAS OAY
16 17 1 0.144 251040.0 0.144 251040.0 ; OAY CAU
17 18 1 0.152 251040.0 0.152 251040.0 ; CAU CAT
18 19 1 0.144 251040.0 0.144 251040.0 ; CAT OAX
19 20 1 0.144 251040.0 0.144 251040.0 ; OAX CAR
20 21 1 0.152 251040.0 0.152 251040.0 ; CAR CAP
21 22 1 0.144 251040.0 0.144 251040.0 ; CAP OAV
22 23 1 0.144 251040.0 0.144 251040.0 ; OAV CAN
23 24 1 0.153 334720.0 0.153 334720.0 ; CAN CAD
24 25 1 0.143 334720.0 0.143 334720.0 ; CAD OAB
25 26 1 0.100 313800.0 0.100 313800.0 ; OAB HAA
[ pairs ]
; ai aj fu c0, c1, ...
1 4 1 ; CAA CAF
2 5 1 ; CAC CAG
3 6 1 ; CAE CAH
4 7 1 ; CAF CAI
5 8 1 ; CAG CAJ
6 9 1 ; CAH CAK
7 10 1 ; CAI CAL
8 11 1 ; CAJ CAM
9 12 1 ; CAK CAO
10 13 1 ; CAL OAW
11 14 1 ; CAM CAQ
12 15 1 ; CAO CAS
13 16 1 ; OAW OAY
14 17 1 ; CAQ CAU
15 18 1 ; CAS CAT
16 19 1 ; OAY OAX
17 20 1 ; CAU CAR
18 21 1 ; CAT CAP
19 22 1 ; OAX OAV
20 23 1 ; CAR CAN
21 24 1 ; CAP CAD
22 25 1 ; OAV OAB
23 26 1 ; CAN HAA
[ angles ]
; ai aj ak fu c0, c1, ...
1 2 3 1 111.0 460.2 111.0 460.2 ; CAA CAC CAE
2 3 4 1 111.0 460.2 111.0 460.2 ; CAC CAE CAF
3 4 5 1 111.0 460.2 111.0 460.2 ; CAE CAF CAG
4 5 6 1 111.0 460.2 111.0 460.2 ; CAF CAG CAH
5 6 7 1 111.0 460.2 111.0 460.2 ; CAG CAH CAI
6 7 8 1 111.0 460.2 111.0 460.2 ; CAH CAI CAJ
7 8 9 1 111.0 460.2 111.0 460.2 ; CAI CAJ CAK
8 9 10 1 111.0 460.2 111.0 460.2 ; CAJ CAK CAL
9 10 11 1 111.0 460.2 111.0 460.2 ; CAK CAL CAM
10 11 12 1 111.0 460.2 111.0 460.2 ; CAL CAM CAO
11 12 13 1 109.5 284.5 109.5 284.5 ; CAM CAO OAW
12 13 14 1 109.5 334.7 109.5 334.7 ; CAO OAW CAQ
13 14 15 1 109.5 284.5 109.5 284.5 ; OAW CAQ CAS
14 15 16 1 109.5 284.5 109.5 284.5 ; CAQ CAS OAY
15 16 17 1 109.5 334.7 109.5 334.7 ; CAS OAY CAU
16 17 18 1 109.5 284.5 109.5 284.5 ; OAY CAU CAT
17 18 19 1 109.5 284.5 109.5 284.5 ; CAU CAT OAX
18 19 20 1 109.5 334.7 109.5 334.7 ; CAT OAX CAR
19 20 21 1 109.5 284.5 109.5 284.5 ; OAX CAR CAP
20 21 22 1 109.5 284.5 109.5 284.5 ; CAR CAP OAV
21 22 23 1 109.5 334.7 109.5 334.7 ; CAP OAV CAN
22 23 24 1 109.5 284.5 109.5 284.5 ; OAV CAN CAD
23 24 25 1 109.5 460.2 109.5 460.2 ; CAN CAD OAB
24 25 26 1 109.5 397.5 109.5 397.5 ; CAD OAB HAA
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
4 3 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih CAF CAE CAC CAA
5 4 3 2 1 0.0 5.9 3 0.0 5.9 3 ; dih CAG CAF CAE CAC
6 5 4 3 1 0.0 5.9 3 0.0 5.9 3 ; dih CAH CAG CAF CAE
7 6 5 4 1 0.0 5.9 3 0.0 5.9 3 ; dih CAI CAH CAG CAF
8 7 6 5 1 0.0 5.9 3 0.0 5.9 3 ; dih CAJ CAI CAH CAG
9 8 7 6 1 0.0 5.9 3 0.0 5.9 3 ; dih CAK CAJ CAI CAH
10 9 8 7 1 0.0 5.9 3 0.0 5.9 3 ; dih CAL CAK CAJ CAI
11 10 9 8 1 0.0 5.9 3 0.0 5.9 3 ; dih CAM CAL CAK CAJ
12 11 10 9 1 0.0 5.9 3 0.0 5.9 3 ; dih CAO CAM CAL CAK
10 11 12 13 1 0.0 5.9 3 0.0 5.9 3 ; dih CAL CAM CAO OAW
11 12 13 14 1 0.0 3.8 3 0.0 3.8 3 ; dih CAM CAO OAW CAQ
15 14 13 12 1 0.0 3.8 3 0.0 3.8 3 ; dih CAS CAQ OAW CAO
13 14 15 16 1 0.0 5.9 3 0.0 5.9 3 ; dih OAW CAQ CAS OAY
14 15 16 17 1 0.0 3.8 3 0.0 3.8 3 ; dih CAQ CAS OAY CAU
18 17 16 15 1 0.0 3.8 3 0.0 3.8 3 ; dih CAT CAU OAY CAS
16 17 18 19 1 0.0 5.9 3 0.0 5.9 3 ; dih OAY CAU CAT OAX
17 18 19 20 1 0.0 3.8 3 0.0 3.8 3 ; dih CAU CAT OAX CAR
21 20 19 18 1 0.0 3.8 3 0.0 3.8 3 ; dih CAP CAR OAX CAT
19 20 21 22 1 0.0 5.9 3 0.0 5.9 3 ; dih OAX CAR CAP OAV
20 21 22 23 1 0.0 3.8 3 0.0 3.8 3 ; dih CAR CAP OAV CAN
24 23 22 21 1 0.0 3.8 3 0.0 3.8 3 ; dih CAD CAN OAV CAP
22 23 24 25 1 0.0 5.9 3 0.0 5.9 3 ; dih OAV CAN CAD OAB
23 24 25 26 1 0.0 1.3 3 0.0 1.3 3 ; dih CAN CAD OAB HAA
**********************************************************************************************
The topology provided here seems to have a low topology quality.
It will be possible to build the topology for C12E4 from the topology of an ether-oxyd, and not a lipid.
Has someone ever build a topology of an ether-oxyd ?
Thank you very much.
Erol
---------------------------------
Appel audio GRATUIT partout dans le monde avec le nouveau Yahoo! Messenger
Téléchargez le ici !
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20051107/af10e2fe/attachment.html>
More information about the gromacs.org_gmx-users
mailing list