[gmx-users] Fw: GDP topology
Michal Kolinski
mkolin at iimcb.gov.pl
Mon Dec 13 13:04:39 CET 2004
Hi all!
I need to simulate rhodopsin in lipid bilayer with G protein + GDP
I'm not certain if the topology file (charges) for GDP I have obtained using PRODRG
server is right for me. I plan to use (ffgmx_lipids.tar.gz) ffgmx force field modified
to use with lipids from gromacs site. (At the beginning I did a short simulation of GDP
in box of water only and everything seemed fine). Please give me some comment and
thank you in advice.
here is part of my gdp.itp file:
[ moleculetype ]
; Name nrexcl
GDP 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 OA 1 GDP O2B 1 -1.144 15.9994
2 P 1 GDP PB 1 1.123 30.9738
3 OA 1 GDP O3B 1 -1.145 15.9994
4 OM 1 GDP O1B 1 -0.834 15.9994
5 OS 1 GDP O3A 2 -0.176 15.9994
6 P 1 GDP PA 2 1.404 30.9738
7 OM 1 GDP O1A 2 -0.526 15.9994
8 OM 1 GDP O2A 2 -0.526 15.9994
9 OS 1 GDP O5* 2 -0.176 15.9994
10 CH2 1 GDP C5* 3 0.034 14.0270
11 CS1 1 GDP C4* 3 0.180 13.0190
12 OS 1 GDP O4* 3 -0.214 15.9994
13 CH1 1 GDP C3* 4 0.133 13.0190
14 OA 1 GDP O3* 4 -0.160 15.9994
15 HO 1 GDP HAA 4 0.027 1.0080
16 CH1 1 GDP C2* 5 0.083 13.0190
17 OA 1 GDP O2* 5 -0.256 15.9994
18 HO 1 GDP HAB 5 0.016 1.0080
19 CS1 1 GDP C1* 5 0.157 13.0190
20 NR5* 1 GDP N9 6 0.119 14.0067
21 CR51 1 GDP C8 6 -0.119 13.0190
22 NR5 1 GDP N7 7 -0.427 14.0067
23 CB 1 GDP C5 7 0.132 12.0110
24 CB 1 GDP C4 7 0.302 12.0110
25 NR6 1 GDP N3 7 -0.438 14.0067
26 CB 1 GDP C2 7 0.431 12.0110
27 NT 1 GDP N2 8 0.039 14.0067
28 H 1 GDP HAE 8 -0.019 1.0080
29 H 1 GDP HAD 8 -0.020 1.0080
30 NR6* 1 GDP N1 9 0.005 14.0067
31 H 1 GDP HAC 9 -0.038 1.0080
32 CB 1 GDP C6 9 0.157 12.0110
33 O 1 GDP O6 9 -1.124 15.9994
[ bonds ]
; ai aj fu c0, c1, ...
1 2 1 0.161 251040.0 0.161 251040.0 ; O2B PB
2 3 1 0.161 251040.0 0.161 251040.0 ; PB O3B
2 4 1 0.148 376560.0 0.148 376560.0 ; PB O1B
2 5 1 0.161 251040.0 0.161 251040.0 ; PB O3A
5 6 1 0.161 251040.0 0.161 251040.0 ; O3A PA
6 7 1 0.148 376560.0 0.148 376560.0 ; PA O1A
6 8 1 0.148 376560.0 0.148 376560.0 ; PA O2A
6 9 1 0.161 251040.0 0.161 251040.0 ; PA O5*
9 10 1 0.143 251040.0 0.143 251040.0 ; O5* C5*
10 11 1 0.153 251040.0 0.153 251040.0 ; C5* C4*
11 12 1 0.144 251040.0 0.144 251040.0 ; C4* O4*
11 13 1 0.153 334720.0 0.153 334720.0 ; C4* C3*
12 19 1 0.144 251040.0 0.144 251040.0 ; O4* C1*
13 14 1 0.143 334720.0 0.143 334720.0 ; C3* O3*
13 16 1 0.153 334720.0 0.153 334720.0 ; C3* C2*
14 15 1 0.100 313800.0 0.100 313800.0 ; O3* HAA
16 17 1 0.143 334720.0 0.143 334720.0 ; C2* O2*
16 19 1 0.153 334720.0 0.153 334720.0 ; C2* C1*
17 18 1 0.100 313800.0 0.100 313800.0 ; O2* HAB
19 20 1 0.148 251040.0 0.148 251040.0 ; C1* N9
20 21 1 0.133 418400.0 0.133 418400.0 ; N9 C8
20 24 1 0.133 418400.0 0.133 418400.0 ; N9 C4
21 22 1 0.133 418400.0 0.133 418400.0 ; C8 N7
22 23 1 0.133 418400.0 0.133 418400.0 ; N7 C5
23 24 1 0.139 418400.0 0.139 418400.0 ; C5 C4
23 32 1 0.139 418400.0 0.139 418400.0 ; C5 C6
24 25 1 0.134 418400.0 0.134 418400.0 ; C4 N3
25 26 1 0.134 418400.0 0.134 418400.0 ; N3 C2
26 27 1 0.133 376560.0 0.133 376560.0 ; C2 N2
26 30 1 0.140 334720.0 0.140 334720.0 ; C2 N1
27 28 1 0.100 374468.0 0.100 374468.0 ; N2 HAE
27 29 1 0.100 374468.0 0.100 374468.0 ; N2 HAD
30 31 1 0.100 374468.0 0.100 374468.0 ; N1 HAC
30 32 1 0.140 334720.0 0.140 334720.0 ; N1 C6
32 33 1 0.123 502080.0 0.123 502080.0 ; C6 O6
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