[gmx-users] sugar building blocks

hugo verli hugo at acd.ufrj.br
Tue Mar 23 20:46:01 CET 2004


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)
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?

Many thanks in advance,

hugo Verli.

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