[gmx-users] dealing with ATP
Itamar Kass
itamar.kass at monash.edu
Mon Apr 25 12:23:27 CEST 2011
ATP is well 'known' and used, just put attention to it protionation state.
Cheers,
Itamar
On 25/04/2011 8:05 PM, Sajad Ahrari wrote:
> 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 <jalemkul at vt.edu>
> *To:* Gromacs Users' List <gmx-users at 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 <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> > *To:* Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at 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><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
>
> ========================================
> -- gmx-users mailing list gmx-users at gromacs.org
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--
"In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut
===========================================
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: Itamar.Kass at monash.edu
============================================
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