[gmx-users] add a group to an amino acid

[Mark Abraham]

On 14/11/2010 8:13 PM, hengame fallah wrote:
>
>
> I read about .hdb file and then i editted my .hdb file:
>
> ...
> BOC 9

Then you'll know from your reading what this number should be :-) It's 
the number of types of hydrogen atoms that might be added. For each of 
them, there's one line below. You needed to have left this on 8. Because 
you've changed it to 9, pdb2gmx tries to make sense of a ninth line, 
which is "CYS2 3" and gives you the error you saw.

Mark

> 1    1    H         N      -C        CA
> 2    6    HA      CA      N       CB
> 1    5    HB      CB     CA      CG1    CG2
> 1    1    HD1    CD1    CG1    CE1
> 1    1    HD2    CD2    CG1    CE2
> 1    1    HE1    CE1    CD1    CZ
> 1    1    HE2    CE2    CD2    CZ
> 2    6    HG     CG2    CB      C
> CYS2    3
> 1    1    H       N    -C       CA
> 1    5    HA    CA    N       C    CB
> 2    6    HB    CB    SG    CA
> ...
> PHE     8
> 1    1    H         N      -C       CA
> 1    5    HA      CA     N       C    CB
> 2    6    HB      CB     CG    CA
> 1    1    HD1    CD1    CG    CE1
> 1    1    HD2    CD2    CG    CE2
> 1    1    HE1    CE1    CD1    CZ
> 1    1    HE2    CE2    CD2    CZ
> 1    1    HZ      CZ      CE1    CE2
> ...
>
> but i got this error:
>
> ...
> There are 1 chains and 0 blocks of water and 3 residues with 63 atoms
>
>   chain  #res #atoms
>   1 ' '     3     63
>
> All occupancy fields zero. This is probably not an X-Ray structure
> Opening library file /usr/share/gromacs/top/ffoplsaa.atp
> Atomtype 1
> Reading residue database... (ffoplsaa)
> Opening library file /usr/share/gromacs/top/ffoplsaa.rtp
> Residue 57
> Sorting it all out...
> Opening library file /usr/share/gromacs/top/ffoplsaa.hdb
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.0.7
> Source code file: ../../../../src/kernel/h_db.c, line: 87
>
> Fatal error:
> wrong format in input file ffoplsaa.hdb on line
> CYS2    3

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