[gmx-users] Sugar topologies

[Lieven Buts]

  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
-----------------------------------------------------------
-------------------------------------------------------------------------

  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:
        -0.548        -0.548
     H6A-O6A-C6A    H6B-O6B-C6B
      HO  OA C       HO OA  C
             |              |
            C5A-O5A       C5B--O5B
            CS1 OS        CS1  OS
            /    \         /    \
   H4A-O4A-C4A   C1A-OG--C4B    C1B--O1B--C7
    HO  OA  C    CS1      C     CS1       CH3
            \    /         \    /
            C3A-C2A        C3B-C2B
            C   C          C   C
            |  |           |  |
           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:



-- 
Lieven Buts
Vrije Universiteit Brussel