[gmx-users] sugar building blocks

[David]

On Tue, 2004-03-23 at 20:43, hugo verli wrote:
> Hi,
> 
> considering the difficulties in using PRODRG for long chain polysaccharides
> I'm trying to made building blocks to some monosaccharides. I suppose that
> with these building blocks I'll be able to generate topologies for long
> polysaccharides composed by these blocks. I am using the GROMACS 3.2.1.
> I created a topology for one monosaccharide (called IDS) using PRODRG and
> inserted its parameters on the ffgmx.rtp file, as follow:
> 
> [ IDS ]
>  [ atoms ]
>    O1S    OA  -0.774     0 
>      S     S   1.612     0
>    O2S    OA  -0.774     0
>    O3S    OA  -0.774     0
>     O2    OS  -O.515     0
>     C2   CH1   0.225     0
>     C3   CH1   0.160     1
>     O3    OA  -0.400     1
>    HO3    HO   0.240     1
>     C4   CH1   0.142     2
>     C5   CS1   0.242     3
>     O5    OS  -0.242     3
>     C6     C   0.172     4
>    O61    OM  -0.586     4
>    O62    OM  -0.586     4
>     C1   CS1   0.254     5
>     O1    OA  -0.396     5
>  [ bonds ]
>    O1S    S
>      S  O2S
>      S  O3S
>      S   O2
>     O2   C2
>     C2   C3
>     C2   C1
>     C3   O3
>     C3   C4
>     O3  HO3
>     C4   C5
>     C5   C6
>     C5   O5
>     C6  O62
>     C6  O61
>     O5   C1
>     C1   O1
>  [ impropers ]
>     C6   C5  O61  O62
>      S  O1S  O2S  O3S
>     C2   O2   C3   C1
>     C3   C2   C4   O3
>     C5   C4   C6   O5
>     C1   C2   O1   O5
>    O1S    S   O2   C2
>      S   O2   C2   C1
>     C4   C3   C2   O2
>     O2   C2   C1   O1
>     C2   C3   O3  HO3
>     C5   C4   C3   C2
>     O5   C5   C4   C3
>     C4   C5   C6  O61
>     C4   C5   O5   C1
>     O1   C1   O5   C5
> 
> However, when I run pdb2gmx I obtain the following error:
> 
> Select the Force Field:
>  0: GROMOS96 43a1 Forcefield (official distribution)
>  1: GROMOS96 43b1 Vacuum Forcefield (official distribution)
>  2: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)
>  3: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
>  4: Gromacs Forcefield (see manual)
>  5: gmx Forcefield with hydrogens for NMR stuff (Do NOT use for new runs)
> 4
> Looking whether force field file ffgmx.rtp exists
> Opening library file /usr/local/share/gromacs/top/ffgmx.rtp
> Opening library file /usr/local/share/gromacs/top/aminoacids.dat
> Reading IdoA.pdb...
> Read 'gmx Forcefield with hydrogens for NMR stuff (Do NOT use for new runs)',
> 22 atoms
> Opening library file /usr/local/share/gromacs/top/xlateat.dat
> 23 out of 23 lines of xlateat.dat converted succesfully
> Analyzing pdb file
> There are 1 chains and 0 blocks of water and 1 residues with 22 atoms
> 
>   chain  #res #atoms
>   1 ' '     1     22  
> 
> All occupancies are one
> Opening library file /usr/local/share/gromacs/top/ffgmx.atp
> Atomtype 54
> Reading residue database... (ffgmx)
> Opening library file /usr/local/share/gromacs/top/ffgmx.rtp
> Residue 52Fatal error: in .rtp file in residue IDS at line:
>     O2    OS  -O.515     0
> 
> The atom appear to be ok, so what is the reason for this error?
> 
try running pdb2gmx -debug and check the pdb2gmx.log file for clues.


> Many thanks in advance,
> 
> hugo Verli.
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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