dear Justin
it seems that, ADP and ATP are not known to any of gromacs forcefields. but
their topologies have been described in amber web site(as follows). should i be
adding them to .tpr file of gromacs? if so, how can i access this file and is
there any modification being needed in what amber has introduced? (or i have to
just do something like copy and paste?)
all the best
sajad
topology for ADP:
0 0 2
R-ADENOSINE - with diphosphate linker
adp.db94
adp INT 1
CORRECT OMIT DU BEG
0.0
1 DUMM DU M 0 0 0 0.000 0.000 0.000 0.000
2 DUMM DU M 1 0 0 1.000 0.000 0.000 0.000
3 DUMM DU M 2 1 0 1.000 90.000 0.000 0.000
4 O1B O3 M 3 2 1 1.000 90.000 180.000 -0.9552
5 PB P M 4 3 2 1.434 90.000 180.000 1.3672
6 O2B O3 E 5 4 3 1.574 107.490 -79.441 -0.9552
7 O3B O3 E 5 4 3 1.518 118.007 165.990 -0.9552
8 O3A OS M 5 4 3 1.599 113.374 180.000 -0.6346
9 PA P M 6 5 4 1.646 130.619 36.624 1.4929
10 O1A O2 E 7 6 5 1.504 109.212 -90.234 -0.9474
11 O2A O2 E 7 6 5 1.526 108.570 40.323 -0.9474
12 O5* OS M 7 6 5 1.585 97.173 157.726 -0.6579
13 C5* CT M 8 7 6 1.445 122.292 -66.317 0.0558
14 H50 H1 E 9 8 7 1.059 109.484 27.531 0.0679
15 H51 H1 E 9 8 7 1.059 109.437 -92.456 0.0679
16 C4* CT M 9 8 7 1.477 113.286 147.538 0.1065
17 H40 H1 E 16 9 8 1.059 105.768 -179.178 0.1174
18 O4* OS S 16 13 9 1.482 106.235 -62.889 -0.3548
19 C1* CT B 18 16 13 1.391 107.688 128.804 0.0394
20 H10 H2 E 19 18 16 1.059 109.468 91.228 0.2007
21 N9 N* S 19 18 16 1.552 105.091 -143.300 -0.0251
22 C8 CK B 21 19 18 1.388 123.797 33.434 0.2006
23 H80 H5 E 22 21 19 1.078 131.047 -3.389 0.1553
24 N7 NB S 22 21 19 1.384 108.967 176.598 -0.6073
25 C5 CB S 24 22 21 1.395 103.021 0.702 0.0515
26 C6 CA B 25 24 22 1.412 128.288 178.252 0.7009
27 N6 N2 B 26 25 24 1.333 125.907 -3.791 -0.9019
28 H60 H E 27 26 25 1.010 120.010 2.829 0.4115
29 H61 H E 27 26 25 1.009 120.014 -177.167 0.4115
30 N1 NC S 26 25 24 1.343 113.319 178.851 -0.7615
31 C2 CQ B 30 26 25 1.340 123.433 -1.664 0.5875
32 H2 H5 E 31 30 26 1.077 120.022 -177.875 0.0473
33 N3 NC S 31 30 26 1.377 125.379 2.123 -0.6997
34 C4 CB E 33 31 30 1.300 108.242 -0.035 0.3053
35 C3* CT M 16 13 12 1.484 117.051 57.581 0.2022
36 H30 H1 E 35 16 13 1.059 117.939 24.820 0.0615
37 O3* OH S 35 16 13 1.407 108.509 149.908 -0.6541
38 H3* HO E 37 35 16 0.967 109.470 163.254 0.4376
39 C2* CT M 35 16 13 1.607 102.425 -96.715 0.0670
40 H20 H1 E 39 35 16 1.059 115.086 78.119 0.0972
41 O2* OH S 39 35 16 1.398 114.943 -153.294 -0.6139
42 H2* HO E 41 39 35 0.967 109.456 -41.679 0.4186
IMPROPER
C8 C4 N9 C1*
C6 H60 N6 H61
N7 N9 C8 H80
N1 N3 C2 H2
topology for ATP:
0 0 2
R-ADENOSINE - with triphosphate linker
atp.db94
atp INT 1
CORRECT OMIT DU BEG
0.0
1 DUMM DU M 0 0 0 1.000 90.000 180.000 0.000
2 DUMM DU M 1 0 0 0.967 90.000 180.000 0.000
3 DUMM DU M 2 1 0 0.967 109.443 180.000 0.000
4 O1G O3 M 3 2 1 1.086 160.811 148.238 -0.9526
5 PG P M 4 3 2 1.379 92.848 -159.681 1.2650
6 O2G O3 E 5 4 3 1.417 116.381 -173.072 -0.9526
7 O3G O3 E 5 4 3 1.443 104.744 40.954 -0.9526
8 O3B OS M 5 4 3 1.742 94.444 -63.733 -0.5322
9 PB P M 8 5 3 1.512 135.464 -125.176 1.3852
10 O1B O2 E 9 8 5 1.415 113.542 -28.935 -0.8894
11 O2B O2 E 9 8 5 1.617 103.881 -164.747 -0.8894
12 O3A OS M 9 8 5 1.734 96.237 83.499 -0.5689
13 PA P M 12 9 8 1.516 131.613 -127.461 1.2532
14 O1A O2 E 13 12 9 1.526 115.352 -92.892 -0.8799
15 O2A O2 E 13 12 9 1.410 109.213 53.806 -0.8799
16 O5* OS M 13 12 9 1.749 97.280 164.349 -0.5987
17 C5* CT M 16 13 12 1.427 117.355 64.264 0.0558
18 H50 H1 E 17 16 13 1.059 109.461 103.970 0.0679
19 H51 H1 E 17 16 13 1.059 109.491 -16.065 0.0679
20 C4* CT M 17 16 13 1.446 107.888 -136.043 0.1065
21 H40 H1 E 20 17 16 1.059 106.572 -167.965 0.1174
22 O4* OS S 20 17 16 1.577 105.136 -48.024 -0.3548
23 C1* CT B 22 20 17 1.562 99.310 148.198 0.0394
24 H10 H2 E 23 22 20 1.059 104.667 127.006 0.2007
25 N9 N* S 23 22 20 1.651 99.707 -129.444 -0.0251
26 C8 CK B 25 23 22 1.400 121.683 69.274 0.2006
27 H80 H5 E 26 25 23 1.077 128.168 2.532 0.1553
28 N7 NB S 26 25 23 1.327 111.806 -177.463 -0.6073
29 C5 CB S 28 26 25 1.365 104.681 2.256 0.0515
30 C6 CA B 29 28 26 1.448 131.894 -177.019 0.7009
31 N6 N2 B 30 29 28 1.312 123.747 -3.485 -0.9019
32 H60 H E 31 30 29 1.000 120.000 176.690 0.4115
33 H61 H E 31 30 29 1.000 120.000 -3.310 0.4115
34 N1 NC S 30 29 28 1.362 114.694 173.408 -0.7615
35 C2 CQ B 34 30 29 1.370 122.869 5.034 0.5875
36 H2 H5 E 35 34 30 1.078 119.995 174.203 0.0473
37 N3 NC S 35 34 30 1.309 125.548 -5.799 -0.6997
38 C4 CB E 37 35 34 1.340 112.610 1.051 0.3053
39 C3* CT M 20 17 16 1.539 120.245 66.848 0.2022
40 H30 H1 E 39 20 17 1.059 109.025 -37.638 0.0615
41 O3* OH S 39 20 17 1.390 114.084 86.172 -0.6541
42 H3' HO E 41 39 20 0.967 109.487 -2.526 0.4376
43 C2* CT M 39 20 17 1.606 106.034 -155.382 0.0670
44 H20 H1 E 43 39 20 1.059 123.901 158.202 0.0972
45 O2* OH S 43 39 20 1.368 107.234 -72.414 -0.6139
46 H2' HO E 45 43 39 0.967 109.442 -16.862 0.4186
IMPROPER
C8 C4 N9 C1*
C6 H60 N6 H61
N7 N9 C8 H80
N1 N3 C2 H2
C5 N1 C6 N6
LOOP CLOSING EXPLICIT
C1* C2*
C4 C5
C4 N9
DONE
STOP
________________________________
From: Justin A. Lemkul <jalem...@vt.edu>
To: Gromacs Users' List <gmx-users@gromacs.org>
Sent: Sat, April 23, 2011 5:46:24 PM
Subject: Re: [gmx-users] dealing with ATP
Sajad Ahrari wrote:
> tnx for your help Justin!
> but shouldn't the topology of S atom be described for gromacs? unless gromacs
>may know P atom with the same topology as S. although they may not be the
>same!?
You're talking about two separate issues - atom types and parameters for
molecules. Yes, most (all?) force fields describe both P and S atoms, but I
guarantee none of them have (by default) parameters for some species named "d"
that represents ADP-SO4. You cannot assign parameters from P blindly to S and
hope for the best. That sounds fundamentally wrong to me.
In your original message, it sounded like you wanted to change ADP-SO4 into
ATP,
but perhaps I misunderstood what you intended. No force field will be able to
assign parameters to ADP-SO4, even though the force field may recognize
individual atoms, it cannot construct a topology for any arbitrary molecules.
If you need to simulation this ADP-SO4 species, you're in for the long road of
parameterization:
http://www.gromacs.org/Documentation/How-tos/Parameterization
Otherwise, change the S atom to P and name the molecule ATP so it will be
recognized by whatever force field you choose, after you have verified that the
force field can indeed recognize such a species. Otherwise, you're stuck doing
parameterization for ATP, too.
-Justin
> regards
> sajad
>
> ------------------------------------------------------------------------
> *From:* Justin A. Lemkul <jalem...@vt.edu>
> *To:* Discussion list for GROMACS users <gmx-users@gromacs.org>
> *Sent:* Sat, April 23, 2011 5:54:58 AM
> *Subject:* Re: [gmx-users] dealing with ATP
>
>
>
> Sajad Ahrari wrote:
> > Dear users
> > i am working with a protein witch holds a hetero-atom in it's pdb
> structure.
>the hetero-atom is named "d" and stands for "ADP+SO4" (in fact the third
>phosphate of ATP is being substituted with SO4). i wanted to know if gromacs
>holds a feature to change "d" into ATP? and if so do
>
> No, but you can use a text editor to replace the S atom with P.
>
> > i need to introduce ATP for Gromacs or it is known for the program?
>
> Some force fields support ATP, some do not. Check the .rtp files and see
> what
>you find.
>
> -Justin
>
> > i do appreciate your help!
> > sajad
> >
>
> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu<http://vt.edu/> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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