[gmx-users] missing atoms

[Mark Abraham]

swatik at ncbs.res.in wrote:
> Hi All,
> 
> I am running Gromacs for drug enzyme complex using AMBER as
> forcefield.While running pdb2gmx command I am getting error and warning of
> 790 missing atoms. Can anybody suggest me how to correct this error.

Either supply a structure file that has suitable hydrogens already built 
in with some external program, or see what the problem is with the AMBER 
.hdb file and your residues named CYSH. The required .hdb format is 
described in Chapter 5 of the manual.

Mark

> error :
> -----------------------------------------------------------
> WARNING: atom H is missing in residue CYSH 703 in the pdb file
>          You might need to add atom H to the hydrogen database of residue
> CYSH
>          in the file ff???.hdb (see the manual)
> 
> 
> WARNING: atom HA is missing in residue CYSH 703 in the pdb file
>          You might need to add atom HA to the hydrogen database of residue
> CYSH
>          in the file ff???.hdb (see the manual)
> 
> 
> WARNING: atom HB1 is missing in residue CYSH 703 in the pdb file
>          You might need to add atom HB1 to the hydrogen database of
> residue CYSH
>          in the file ff???.hdb (see the manual)
> 
> 
> WARNING: atom HB2 is missing in residue CYSH 703 in the pdb file
>          You might need to add atom HB2 to the hydrogen database of
> residue CYSH
>          in the file ff???.hdb (see the manual)
> 
> -------------------------------------------------------
> Program pdb2gmx_mpi, VERSION 3.3.1
> Source code file: pdb2top.c, line: 697
> 
> Fatal error:
> There were 790 missing atoms in molecule Protein_A, if you want to use
> this incomplete topology anyhow, use the option -missing
> -------------------------------------------------------
> 
> 
> 
> 
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