[gmx-users] missing atoms

[Kukol, Andreas]

It is not straightforward to use the AMBER forcefield with Gromacs. You need to edit your pdb-file to account for different atom/residue names used by AMBER as opposed to GROMOS forcefields.
Detailed info is here: http://chemistry.csulb.edu/ffamber/

If this is your first MD simulation, try things with one of the Gromos forcefields first.

Andreas

> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of swatik at ncbs.res.in
> Sent: 29 May 2009 10:21
> To: gmx-users at gromacs.org
> Subject: [gmx-users] missing atoms
>
> 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.
>
> 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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