[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
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>
##############################################################################
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
O C O C Visit the PRODRG server to take
" | " | the stress out of your topologies!
N--c--C--N--C--C--N--C--C--N--C--C--O
| " | " http://davapc1.bioch.dundee.ac.uk/
C-C-O O C-C-C O programs/prodrg/prodrg.html
"
O
More information about the gromacs.org_gmx-users
mailing list