[gmx-users] dealing with ATP

Sajad Ahrari sajadahrari at yahoo.com
Mon Apr 25 12:05:25 CEST 2011


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>
> *To:* Discussion list for GROMACS users <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/> | (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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