[gmx-users] Sugar topologies (complete message)

Daan van Aalten dava at davapc1.bioch.dundee.ac.uk
Thu Jan 31 10:48:54 CET 2002


Hi Lieven

My understanding of sugars in GMX/GROMOS was that the CSx atom types were
only for the carbons neighbouring the ether oxygen. If this turns out not
to be the case, it's very easy to change all the pyranose carbon atom
types into their Cx equivalents in PRODRG.
Let me know if you find the answer to this problem.

cheers

Daan



On Thu, 31 Jan 2002, Lieven Buts wrote:

> 
>   (Apologies for posting an incomplete version of this message
>    earlier.)
> 
>   Hello all,
> 
>   I am trying to use Gromacs 3.0 to study the confromational 
> properties of sugars in solution and bound to proteins. Initially
> I wanted to make topology building blocks (analogous to to the 
> amino acid building blocks) but now I think it might be
> simpler to use PRODRG to generate topologies for the sugars I
> need.
>   As a test case I used the mannose(alpha1,4)mannose(alpha1-)methyl
> disaccharide:
> 
> ----- m4m.pdb -------------------------------------------------------
> ATOM   3714  C1  MAN S   1       4.529  42.024  25.677  1.00 27.07
> ATOM   3715  C2  MAN S   1       3.472  41.123  25.039  1.00 27.92
> ATOM   3716  O2  MAN S   1       4.061  40.375  23.988  1.00 29.21
> ATOM   3717  C3  MAN S   1       2.906  40.171  26.094  1.00 26.40
> ATOM   3718  O3  MAN S   1       1.970  39.287  25.497  1.00 27.87
> ATOM   3719  C4  MAN S   1       4.035  39.372  26.738  1.00 21.18
> ATOM   3720  O4  MAN S   1       3.505  38.578  27.784  1.00 23.26
> ATOM   3721  C5  MAN S   1       5.094  40.327  27.303  1.00 25.69
> ATOM   3722  O5  MAN S   1       5.555  41.228  26.268  1.00 24.50
> ATOM   3723  C6  MAN S   1       6.311  39.595  27.841  1.00 22.90
> ATOM   3724  O6  MAN S   1       7.080  39.028  26.790  1.00 20.69
> ATOM   3725  C1  MAN S   2       4.412  46.882  27.747  1.00 47.19
> ATOM   3726  O1  MAN S   2       3.168  46.841  28.357  1.00 51.01
> ATOM   3727  C2  MAN S   2       4.251  46.618  26.248  1.00 45.91
> ATOM   3728  O2  MAN S   2       5.515  46.713  25.609  1.00 49.07
> ATOM   3729  C3  MAN S   2       3.669  45.220  26.031  1.00 44.04
> ATOM   3730  O3  MAN S   2       3.604  44.936  24.641  1.00 49.15
> ATOM   3731  C4  MAN S   2       4.536  44.175  26.730  1.00 39.76
> ATOM   3732  O4  MAN S   2       3.920  42.881  26.599  1.00 32.21
> ATOM   3733  C5  MAN S   2       4.683  44.537  28.211  1.00 42.72
> ATOM   3734  O5  MAN S   2       5.239  45.868  28.345  1.00 44.76
> ATOM   3735  C6  MAN S   2       5.596  43.581  28.963  1.00 42.20
> ATOM   3736  O6  MAN S   2       6.925  44.075  29.036  1.00 43.13
> ATOM   3737  C7  AME S   3       2.916  47.854  29.323  1.00 53.95
> END
> ---------------------------------------------------------------------
> 
>   PRODRG returned a Gromacs topology file. I modified the residue and 
> atom names to something a little more meaningful (for me):
> 
> ----- m4mh.top-------------------------------------------------------
>  [ defaults ]
>  ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
>    1             1               no              1.0     1.0
> #include "ffgmx.itp"
> #include "spc.itp"
> 
>  [ moleculetype ]
>  ;name nrexcl
> M4MM      3
> 
> ...
> 
>  [ atoms ]
>  ;  nr  type resnr resid  atom  cgnr charge
>      1    HO     1 M4MM     H2A     1    0.000
>      2    OA     1 M4MM     O2A     2    0.000
>      3   CH1     1 M4MM     C2A     3    0.000
>      4   CH1     1 M4MM     C3A     4    0.150
>      5    OA     1 M4MM     O3A     4   -0.548
>      6    HO     1 M4MM     H3A     4    0.398
>      7   CH1     1 M4MM     C4A     5    0.150
>      8    OA     1 M4MM     O4A     5   -0.548
>      9    HO     1 M4MM     H4A     5    0.398
>     10   CS1     1 M4MM     C5A     6    0.000
>     11   CH2     1 M4MM     C6A     7    0.150
>     12    OA     1 M4MM     O6A     7   -0.548
>     13    HO     1 M4MM     H6A     7    0.398
>     14    OS     1 M4MM     O5A     8    0.000
>     15   CS1     1 M4MM     C1A     9    0.180
>     16    OS     1 M4MM     OG      9   -0.360
>     17   CS1     1 M4MM     C4B     9    0.180
>     18   CH1     1 M4MM     C3B    10    0.150
>     19    OA     1 M4MM     O3B    10   -0.548
>     20    HO     1 M4MM     H3B    10    0.398
>     21   CH1     1 M4MM     C2B    11    0.150
>     22    OA     1 M4MM     O2B    11   -0.548
>     23    HO     1 M4MM     H2B    11    0.398
>     24   CS1     1 M4MM     C1B    12    0.180
>     25    OS     1 M4MM     O1B    12   -0.360
>     26   CH3     1 M4MM     C7     12    0.180
>     27    OS     1 M4MM     O5B    13    0.000
>     28   CS1     1 M4MM     C5B    14    0.000
>     29   CH2     1 M4MM     C6B    15    0.150
>     30    OA     1 M4MM     O6B    15   -0.548
>     31    HO     1 M4MM     H6B    15    0.398
> 
>  [ bonds ]
>  ;ai  aj  fu    c0          c1
>    1   2   1 0.100    313800.0 0.100    313800.0 ;   HAA  OAC
>      ...
>   30  31   1 0.100    313800.0 0.100    313800.0 ;   OAW  HAG
>  [ pairs ]
>   ;ai  aj  fu    c0          c1
>    1   4   1                   ;   HAA  OAC
>      ...
>   28  31   1                   ;   OAM  CAX
>  [ angles ]
>  ;ai  aj  ak  fu    c0          c1
>    1   2   3   1 109.5       397.5 109.5       397.5 ;   HAA  OAC  CAB
>      ...
>   29  30  31   1 109.5       397.5 109.5       397.5 ;   CAV  OAW  HAG
>  [ dihedrals ]
>  ;ai  aj  ak  al  fu    c0    c1 m  c0   c1 m
>    3   2  15   4   2  35.3  836.8 0  35.3  836.8 0 ; IDI   CAB  OAC 
> CAA  CAD
>      ... 
>   28  29  30  31   1   0.0    1.3 3   0.0    1.3 3 ; DI    CAT  CAV 
> OAW  HAG
> 
>  [ system ]
>  ManA4Man
> 
>  [ molecules ]
>  M4MM 1
> ---------------------------------------------------------------------------
> 
>   I removed the "SOL  0" line, since genbox just adds an additional
> "SOL  <n>" line at the end.
> 
>   This topology corresponds to the following (atom types given
> below the atom names):
> 
>      H6A-O6A-C6A    H6B-O6B-C6B
>       HO  OA CH2     HO OA  CH2
>              |              |
>             C5A-O5A       C5B--O5B
>             CS1 OS        CS1  OS
>             /    \         /    \
>    H4A-O4A-C4A   C1A-OG--C4B    C1B--O1B--C7
>     HO  OA CH1   CS1 OS  CH1    CS1  OS   CH3
>             \    /         \    /
>             C3A-C2A        C3B-C2B
>             CH1 CH1        CH1 CH1
>             |   |           |  |
>            O3A  O2A        O3B O2B
>             OA  OA          OA OA
>              |  |           |  |
>             H3A H2A       H3B  H2B
>              HO HO         HO  HO
> 
>   I compared this to the topology for glucose (an
> isomer of mannose) in ${gromacs}/share/top/ffgmx.rtp :
> 
>  H6--O6--C6
>  HO  OA  CS2       
>           |
>          C5---O5
>          CS1  OS
>         /       \
>     O4-C4        C1
>     OS CS1       CS1
>         \       /
>          C3----C2
>          CS1   CS1
>          |     |
>          O3    O2
>          OA    OA
>          |     |
>          H3    H2
>          HO    HO
> 
>   This is probably intended as a building block for
> a 1-4 glucose polymer. The biggest difference is that
> the C2, C3 and C4 atoms are of type CS1 instead of CH1
> as in the PRODRG topology, and the C6 atoms are CS2
> instead of CH2. If I understand correctly, the CS1 and
> CS2 atom types were introduced to better model specific
> sugar effects such as the exo-anomeric effect.
>   Would it be necessary to replace the CH types by
> the corresponding CS types? 
> 
> -- 
> Lieven Buts
> Vrije Universiteit Brussel
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##############################################################################
 
Dr. Daan van Aalten                    Wellcome Trust RCD Fellow 
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979 
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764 
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk 

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