- Posts: 4
Visualising a CG lipid (RAMP LPS) in VMD one atom appears twice in list
- anna_banana
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2 months 2 weeks ago #9754
by anna_banana
Visualising a CG lipid (RAMP LPS) in VMD one atom appears twice in list was created by anna_banana
Hello, following the reccomended steps on the tutorial to visualise a CG lipid in VMD, I've found this works for all lipids except from RAMP LPS.
My topology:
#include "martini_v2.2.itp"
;#include "martini_v2.0_lipids_all_201506.itp"
;#include "martini_v2.0_ions.itp"
;#include "S4.itp"
#include "RAMP.itp"
[ molecules ]
; name number
RAMP 192
I have just included only the RAMP section of the itp but I'm still having struggles! Please help!
Error: one atom appears twice in list
I am writing: cg_bonds -top S4_test_RAMP.top
My topology:
#include "martini_v2.2.itp"
;#include "martini_v2.0_lipids_all_201506.itp"
;#include "martini_v2.0_ions.itp"
;#include "S4.itp"
#include "RAMP.itp"
[ molecules ]
; name number
RAMP 192
I have just included only the RAMP section of the itp but I'm still having struggles! Please help!
Error: one atom appears twice in list
I am writing: cg_bonds -top S4_test_RAMP.top
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- anna_banana
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- Posts: 4
2 months 2 weeks ago #9755
by anna_banana
Replied by anna_banana on topic Visualising a CG lipid (RAMP LPS) in VMD one atom appears twice in list
The RAMP.itp file is:
[ moleculetype ]
;molecule name nrexcl
RAMP 1
[ atoms ]
; num beadtype resnr resnm bead chrg# charge mass
1 Qa 1 RAMP PO1 1 -2.0000
2 P2 1 RAMP GM1 2 0.0000
3 Nda 1 RAMP GM2 3 0.0000
4 P1 1 RAMP GM3 4 0.0000
5 P2 1 RAMP GM4 5 0.0000
6 P1 1 RAMP GM5 6 0.0000
7 Nda 1 RAMP GM6 7 0.0000
8 Qa 1 RAMP PO2 8 -2.0000
9 Na 1 RAMP GL1 9 0.0000
10 Na 1 RAMP GL2 10 0.0000
11 C1 1 RAMP C1A 11 0.0000
12 C1 1 RAMP C2A 12 0.0000
13 C1 1 RAMP C3A 13 0.0000
14 C1 1 RAMP C1B 14 0.0000
15 C1 1 RAMP C2B 15 0.0000
16 C1 1 RAMP C3B 16 0.0000
17 Na 1 RAMP GL3 17 0.0000
18 Na 1 RAMP GL4 18 0.0000
19 C1 1 RAMP C1C 19 0.0000
20 C1 1 RAMP C2C 20 0.0000
21 C1 1 RAMP C3C 21 0.0000
22 C1 1 RAMP C1D 22 0.0000
23 C1 1 RAMP C2D 23 0.0000
24 C1 1 RAMP C3D 24 0.0000
25 Na 1 RAMP GL5 25 0.0000
26 Nda 1 RAMP GL6 26 0.0000
27 C1 1 RAMP C1E 27 0.0000
28 C1 1 RAMP C2E 28 0.0000
29 Na 1 RAMP GL7 29 0.0000
30 Nda 1 RAMP GL8 30 0.0000
31 C1 1 RAMP C1F 31 0.0000
32 C1 1 RAMP C2F 32 0.0000
33 Qa 1 RAMP S01 33 -1.0000
34 SC1 1 RAMP S02 34 0.0000
35 SN0 1 RAMP S03 35 0.0000
36 P2 1 RAMP S04 36 0.0000
37 P4 1 RAMP S05 37 0.0000
38 SC1 1 RAMP S06 38 0.0000
39 P2 1 RAMP S07 39 0.0000
40 SN0 1 RAMP S08 40 0.0000
41 P4 1 RAMP S09 41 0.0000
42 Qa 1 RAMP S10 42 -1.0000
43 SP1 1 RAMP S11 43 0.0000
44 SN0 1 RAMP S12 44 0.0000
45 P1 1 RAMP S13 45 0.0000
46 P4 1 RAMP S14 46 0.0000
47 Qa 1 RAMP S15 47 -2.0000
48 SP1 1 RAMP S16 48 0.0000
49 SN0 1 RAMP S17 49 0.0000
50 P2 1 RAMP S18 50 0.0000
51 Qa 1 RAMP S19 51 -2.0000
52 SN0 1 RAMP S20 52 0.0000
53 SC1 1 RAMP S21 53 0.0000
54 SN0 1 RAMP S22 54 0.0000
55 P2 1 RAMP S23 55 0.0000
56 P4 1 RAMP S24 56 0.0000
57 SP1 1 RAMP S25 57 0.0000
58 P1 1 RAMP S26 58 0.0000
59 P4 1 RAMP S27 59 0.0000
60 SP1 1 RAMP S28 60 0.0000
61 P1 1 RAMP S29 61 0.0000
62 P4 1 RAMP S30 62 0.0000
63 SP1 1 RAMP S31 63 0.0000
64 P4 1 RAMP S32 64 0.0000
65 P1 1 RAMP S33 65 0.0000
66 SP1 1 RAMP S34 66 0.0000
67 P1 1 RAMP S35 67 0.0000
68 P4 1 RAMP S36 68 0.0000
69 SP1 1 RAMP S37 69 0.0000
70 P1 1 RAMP S38 70 0.0000
71 P4 1 RAMP S39 71 0.0000
[ moleculetype ]
;molecule name nrexcl
RAMP 1
[ atoms ]
; num beadtype resnr resnm bead chrg# charge mass
1 Qa 1 RAMP PO1 1 -2.0000
2 P2 1 RAMP GM1 2 0.0000
3 Nda 1 RAMP GM2 3 0.0000
4 P1 1 RAMP GM3 4 0.0000
5 P2 1 RAMP GM4 5 0.0000
6 P1 1 RAMP GM5 6 0.0000
7 Nda 1 RAMP GM6 7 0.0000
8 Qa 1 RAMP PO2 8 -2.0000
9 Na 1 RAMP GL1 9 0.0000
10 Na 1 RAMP GL2 10 0.0000
11 C1 1 RAMP C1A 11 0.0000
12 C1 1 RAMP C2A 12 0.0000
13 C1 1 RAMP C3A 13 0.0000
14 C1 1 RAMP C1B 14 0.0000
15 C1 1 RAMP C2B 15 0.0000
16 C1 1 RAMP C3B 16 0.0000
17 Na 1 RAMP GL3 17 0.0000
18 Na 1 RAMP GL4 18 0.0000
19 C1 1 RAMP C1C 19 0.0000
20 C1 1 RAMP C2C 20 0.0000
21 C1 1 RAMP C3C 21 0.0000
22 C1 1 RAMP C1D 22 0.0000
23 C1 1 RAMP C2D 23 0.0000
24 C1 1 RAMP C3D 24 0.0000
25 Na 1 RAMP GL5 25 0.0000
26 Nda 1 RAMP GL6 26 0.0000
27 C1 1 RAMP C1E 27 0.0000
28 C1 1 RAMP C2E 28 0.0000
29 Na 1 RAMP GL7 29 0.0000
30 Nda 1 RAMP GL8 30 0.0000
31 C1 1 RAMP C1F 31 0.0000
32 C1 1 RAMP C2F 32 0.0000
33 Qa 1 RAMP S01 33 -1.0000
34 SC1 1 RAMP S02 34 0.0000
35 SN0 1 RAMP S03 35 0.0000
36 P2 1 RAMP S04 36 0.0000
37 P4 1 RAMP S05 37 0.0000
38 SC1 1 RAMP S06 38 0.0000
39 P2 1 RAMP S07 39 0.0000
40 SN0 1 RAMP S08 40 0.0000
41 P4 1 RAMP S09 41 0.0000
42 Qa 1 RAMP S10 42 -1.0000
43 SP1 1 RAMP S11 43 0.0000
44 SN0 1 RAMP S12 44 0.0000
45 P1 1 RAMP S13 45 0.0000
46 P4 1 RAMP S14 46 0.0000
47 Qa 1 RAMP S15 47 -2.0000
48 SP1 1 RAMP S16 48 0.0000
49 SN0 1 RAMP S17 49 0.0000
50 P2 1 RAMP S18 50 0.0000
51 Qa 1 RAMP S19 51 -2.0000
52 SN0 1 RAMP S20 52 0.0000
53 SC1 1 RAMP S21 53 0.0000
54 SN0 1 RAMP S22 54 0.0000
55 P2 1 RAMP S23 55 0.0000
56 P4 1 RAMP S24 56 0.0000
57 SP1 1 RAMP S25 57 0.0000
58 P1 1 RAMP S26 58 0.0000
59 P4 1 RAMP S27 59 0.0000
60 SP1 1 RAMP S28 60 0.0000
61 P1 1 RAMP S29 61 0.0000
62 P4 1 RAMP S30 62 0.0000
63 SP1 1 RAMP S31 63 0.0000
64 P4 1 RAMP S32 64 0.0000
65 P1 1 RAMP S33 65 0.0000
66 SP1 1 RAMP S34 66 0.0000
67 P1 1 RAMP S35 67 0.0000
68 P4 1 RAMP S36 68 0.0000
69 SP1 1 RAMP S37 69 0.0000
70 P1 1 RAMP S38 70 0.0000
71 P4 1 RAMP S39 71 0.0000
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