[gmx-users] GDP and GTP topologies
Ruben M Buey
ruben at akilonia.cib.csic.es
Fri May 13 10:30:22 CEST 2005
Dear Sekar,
My apologies for not replying before. I had forgotten it. Sorry again!
I attach the topology building block of GTP/GDP for 43a1 GROMOS96
forcefield that we have used in our simulations. I hope this will be
useful for you.
Please, do not hesitate to contact me again if you need further help.
Bests,
Ruben
On Sun, 2005-05-01 at 20:08 -0700, Sekar Ramachandran wrote:
> Dear All,
> I am looking for GROMOS96 topology files for GDP and
> GTP. I would be really grateful if someone has already
> built them and provide me with the same.
> Thanks a lot in advance.
> Ram
>
>
> Sekar Ramachandran
> Research Associate
> 316 Baker Laboratories
> DEpartment of Chemistry and Chemical Biology
> Cornell University
> Ithaca 14853
> phone:607-254-6767
-------------- next part --------------
MTBUILDBLSOLUTE
# building block (residue, nucleotide, etc.)
# RNME
GTP
# number of atoms, number of preceding exclusions
# NMAT,NLIN
38 0
# preceding exclusions
#ATOM MAE MSAE
# atoms
#ATOM ANM IACM MASS CGMICGM MAE MSAE
1 O5* 3 16 -0.36000 0 6 2 3 4 5 15 16
2 PA 27 31 0.70500 0 4 3 4 5 6
3 O1A 2 16 -0.63500 0 2 4 5
4 O2A 2 16 -0.63500 1 1 5
5 O3A 3 16 -0.36000 0 4 6 7 8 9
6 PB 27 31 0.70500 0 4 7 8 9 10
7 O1B 2 16 -0.63500 0 2 8 9
8 O2B 2 16 -0.63500 1 1 9
9 O3B 3 16 -0.36000 0 5 10 11 12 13 14
10 PG 27 31 0.63000 0 4 11 12 13 14
11 O1G 2 16 -0.63500 0 3 12 13 14
12 O2G 2 16 -0.63500 0 2 13 14
13 O3G 3 16 -0.54800 0 1 14
14 H3PG 18 1 0.39800 1 0
15 C5* 13 4 0.00000 1 3 16 17 36
16 C4* 12 3 0.16000 0 5 17 18 33 36 37
17 O4* 3 16 -0.36000 0 4 18 19 33 36
18 C1* 12 3 0.20000 1 9 19 20 21 30 31 32 33 34
37
19 N9 8 14 -0.20000 0 8 20 21 22 28 30 31 32 33
20 C4 11 12 0.20000 1 9 21 22 23 26 28 29 30 31
32
21 N3 8 14 -0.36000 0 8 22 23 26 27 28 30 31 32
22 C2 11 12 0.36000 1 8 23 24 25 26 27 28 29 30
23 N2 6 14 -0.83000 0 5 24 25 26 27 28
24 H1N2 18 1 0.41500 0 1 25
25 H2N2 18 1 0.41500 1 0
26 N1 8 14 -0.28000 0 5 27 28 29 30 31
27 H1N1 18 1 0.28000 1 3 28 29 30
28 C6 11 12 0.38000 0 4 29 30 31 32
29 O6 1 16 -0.38000 1 2 30 31
30 C5 11 12 0.00000 0 2 31 32
31 N7 8 14 -0.36000 0 1 32
32 C8 16 3 0.36000 1 0
33 C2* 12 3 0.15000 0 4 34 35 36 37
34 O2* 3 16 -0.54800 0 2 35 36
35 H1O2* 18 1 0.39800 1 0
36 C3* 12 3 0.15000 0 2 37 38
37 O3* 3 16 -0.54800 0 1 38
38 H1O3* 18 1 0.39800 1 0
# trailing atoms
#ATOM ANM IACM MASS CGMICGM
# bonds
# NB
40
# IB JB MCB
1 2 27
1 15 19
2 3 23
2 4 23
2 5 27
5 6 27
6 7 23
6 8 23
6 9 27
9 10 27
# 10
10 11 23
10 12 23
10 13 27
13 14 1
15 16 25
16 17 19
16 36 25
17 18 19
18 19 21
18 33 25
# 20
19 20 9
19 32 9
20 21 11
20 30 15
21 22 11
22 23 8
22 26 16
23 24 2
23 25 2
26 27 2
# 30
26 28 16
28 29 4
28 30 15
30 31 9
31 32 9
33 34 19
34 35 1
33 36 25
36 37 19
37 38 1
# bond angles
# NBA
62
# IB JB KB MCB
1 2 3 13
1 2 4 13
1 2 5 4
1 15 16 8
2 1 15 25
3 2 4 28
3 2 5 13
4 2 5 13
2 5 6 25
5 6 7 13
# 10
5 6 8 13
5 6 9 4
7 6 8 28
7 6 9 13
8 6 9 13
6 9 10 25
9 10 11 13
9 10 12 13
9 10 13 4
11 10 12 28
# 20
11 10 13 13
12 10 13 13
10 13 14 11
15 16 17 8
15 16 36 7
17 16 36 8
16 17 18 9
17 18 19 8
17 18 33 8
19 18 33 8
# 30
18 19 20 36
18 19 32 36
20 19 32 6
19 20 21 38
19 20 30 6
21 20 30 26
20 21 22 26
21 22 23 26
21 22 26 26
23 22 26 26
# 40
22 23 24 22
22 23 25 22
24 23 25 23
22 26 27 24
22 26 28 26
27 26 28 24
26 28 29 26
26 28 30 26
29 28 30 26
20 30 28 26
# 50
20 30 31 6
28 30 31 38
30 31 32 6
19 32 31 6
18 33 36 7
18 33 34 8
34 33 36 8
33 34 35 11
16 36 33 7
16 36 37 8
# 60
33 36 37 8
36 37 38 11
# improper dihedrals
# NIDA
22
# IB JB KB LB MCB
16 17 15 36 2
36 33 37 16 2
18 19 17 33 2
19 32 20 18 1
20 19 32 31 1
32 19 20 30 1
19 32 31 30 1
19 20 30 31 1
32 31 30 20 1
20 19 21 30 1
# 10
30 28 31 20 1
21 20 30 28 1
20 30 28 26 1
30 20 21 22 1
30 28 26 22 1
20 21 22 26 1
21 22 26 28 1
22 26 21 23 1
23 24 25 22 1
26 28 22 27 1
# 20
28 30 26 29 1
33 34 36 18 2
# dihedrals
# NDA
34
# IB JB KB LB MCB
1 15 16 36 17
1 15 16 36 7
1 15 16 17 8
16 15 1 2 14
15 1 2 5 11
15 1 2 5 9
1 2 5 6 11
1 2 5 6 9
2 5 6 9 11
2 5 6 9 9
# 10
5 6 9 10 11
5 6 9 10 9
6 9 10 13 11
6 9 10 13 9
9 10 13 14 11
9 10 13 14 9
15 16 36 33 17
15 16 36 37 7
17 16 36 33 7
17 16 36 37 8
# 20
16 36 33 18 17
37 36 33 18 7
16 36 33 34 7
37 36 33 34 8
36 33 18 17 17
36 33 18 17 7
34 33 18 19 7
34 33 18 17 8
18 33 34 35 12
36 16 17 18 14
# 30
16 17 18 33 14
17 18 19 20 6
21 22 23 24 4
16 36 37 38 12
END
MTBUILDBLSOLUTE
# building block (residue, nucleotide, etc.)
# RNME
GDP
# number of atoms, number of preceding exclusions
# NMAT,NLIN
34 0
# preceding exclusions
#ATOM MAE MSAE
# atoms
#ATOM ANM IACM MASS CGMICGM MAE MSAE
1 O5* 3 16 -0.36000 0 6 2 3 4 5 11 12
2 PA 27 31 0.70500 0 4 3 4 5 6
3 O1A 2 16 -0.63500 0 2 4 5
4 O2A 2 16 -0.63500 1 1 5
5 O3A 3 16 -0.36000 0 5 6 7 8 9 10
6 PB 27 31 0.63000 0 4 7 8 9 10
7 O1B 2 16 -0.63500 0 3 8 9 10
8 O2B 2 16 -0.63500 0 2 9 10
9 O3B 3 16 -0.54800 0 1 10
10 H3PB 18 1 0.39800 1 0
11 C5* 13 4 0.00000 1 3 12 15 32
12 C4* 12 3 0.16000 0 5 13 14 29 32 33
13 O4* 3 16 -0.36000 0 4 14 15 29 32
14 C1* 12 3 0.20000 1 9 15 16 17 26 27 28 29 30
33
15 N9 8 14 -0.20000 0 8 16 17 18 24 26 27 28 29
16 C4 11 12 0.20000 1 9 17 18 19 22 24 25 26 27
28
17 N3 8 14 -0.36000 0 8 18 19 22 23 24 26 27 28
18 C2 11 12 0.36000 1 8 19 20 21 22 23 24 25 26
19 N2 6 14 -0.83000 0 5 20 21 22 23 24
20 H1N2 18 1 0.41500 0 1 21
21 H2N2 18 1 0.41500 1 0
22 N1 8 14 -0.28000 0 5 23 24 25 26 27
23 H1N1 18 1 0.28000 1 3 24 25 26
24 C6 11 12 0.38000 0 4 25 26 27 28
25 O6 1 16 -0.38000 1 2 26 27
26 C5 11 12 0.00000 0 2 27 28
27 N7 8 14 -0.36000 0 1 28
28 C8 16 3 0.36000 1 0
29 C2* 12 3 0.15000 0 4 30 31 32 33
30 O2* 3 16 -0.54800 0 2 31 32
31 H1O2* 18 1 0.39800 1 0
32 C3* 12 3 0.15000 0 2 33 34
33 O3* 3 16 -0.54800 0 1 34
34 H1O3* 18 1 0.39800 1 0
# trailing atoms
#ATOM ANM IACM MASS CGMICGM
# bonds
# NB
36
# IB JB MCB
1 2 27
1 11 19
2 3 23
2 4 23
2 5 27
5 6 27
6 7 23
6 8 23
6 9 27
9 10 1
# 10
11 12 25
12 13 19
12 32 25
13 14 19
14 15 21
14 29 25
15 16 9
15 28 9
16 17 11
16 26 15
# 20
17 18 11
18 19 8
18 22 16
19 20 2
19 21 2
22 23 2
22 24 16
24 25 4
24 26 15
26 27 9
# 30
27 28 9
29 30 19
30 31 1
29 32 25
32 33 19
33 34 1
# bond angles
# NBA
55
# IB JB KB MCB
1 2 3 13
1 2 4 13
1 2 5 4
1 11 12 8
2 1 11 25
3 2 4 28
3 2 5 13
4 2 5 13
2 5 6 25
5 6 7 13
# 10
5 6 8 13
5 6 9 4
7 6 8 28
7 6 9 13
8 6 9 13
6 9 10 11
11 12 13 8
11 12 32 7
13 12 32 8
12 13 14 9
# 20
13 14 15 8
13 14 29 8
15 14 29 8
14 15 16 36
14 15 28 36
16 15 28 6
15 16 17 38
15 16 26 6
17 16 26 26
16 17 18 26
# 30
17 18 19 26
17 18 22 26
19 18 22 26
18 19 20 22
18 19 21 22
20 19 21 23
18 22 23 24
18 22 24 26
23 22 24 24
22 24 25 26
# 40
22 24 26 26
25 24 26 26
16 26 24 26
16 26 27 6
24 26 27 38
26 27 28 6
15 28 27 6
14 29 32 7
14 29 30 8
30 29 32 8
# 50
29 30 31 11
12 32 29 7
12 32 33 8
29 32 33 8
32 33 34 11
# improper dihedrals
# NIDA
22
# IB JB KB LB MCB
12 13 11 32 2
32 29 33 12 2
14 15 13 29 2
15 28 16 14 1
16 15 28 27 1
28 15 16 26 1
15 28 27 26 1
15 16 26 27 1
28 27 26 16 1
16 15 17 26 1
# 10
26 24 27 16 1
17 16 26 24 1
16 26 24 22 1
26 16 17 18 1
26 24 22 18 1
16 17 18 22 1
17 18 22 24 1
18 22 17 19 1
19 20 21 18 1
22 24 18 23 1
# 20
24 26 22 25 1
29 30 32 14 2
# dihedrals
# NDA
30
# IB JB KB LB MCB
1 11 12 32 17
1 11 12 32 7
1 11 12 13 8
12 11 1 2 14
11 1 2 5 11
11 1 2 5 9
1 2 5 6 11
1 2 5 6 9
2 5 6 9 11
2 5 6 9 9
# 10
5 6 9 10 11
5 6 9 10 9
11 12 32 29 17
11 12 32 33 7
13 12 32 29 7
13 12 32 33 8
12 32 29 14 17
33 32 29 14 7
12 32 29 30 7
33 32 29 30 8
# 20
32 29 14 13 17
32 29 14 13 7
30 29 14 15 7
30 29 14 13 8
14 29 30 31 12
32 12 13 14 14
12 13 14 29 14
13 14 15 16 6
17 18 19 20 4
12 32 33 34 12
END
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