[gmx-users] dealing with ATP
Mark Abraham
Mark.Abraham at anu.edu.au
Mon Apr 25 12:26:24 CEST 2011
On 4/25/2011 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?)
This is doable, but there's probably no automatic conversion software,
because nobody's needed to do this so often that writing software was
worthwhile. So you'll have to spend some time with the AMBER and GROMACS
documentation, to learn how to do the conversion of the parameters and
functions between different file formats.
Mark
> 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
> >
> > ========================================
> > -- gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org> <mailto:gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> -- ========================================
>
> 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
> <mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110425/35c7744f/attachment.html>
More information about the gromacs.org_gmx-users
mailing list