[gmx-users] Heme group with CHARMM27 FF

[Mark Abraham]

On 20/04/2012 2:33 PM, Sundar Jubilant wrote:
> Dear gmx-users,
>
> I am new to Gromacs and trying to simulate a protein with a heme group 
> using CHARMM27 ff in Gromacs 4.5.3. I have received the following 
> error while running pdb2gmx .

When asking for help, please give your full command lines and/or 
interactive selections so that we can know more context.

>
> WARNING: atom HA is missing in residue HEM 513 in the pdb file
>          You might need to add atom HA to the hydrogen database of 
> building block HEME
>          in the file aminoacids.hdb (see the manual)
>
>
> WARNING: atom HB is missing in residue HEM 513 in the pdb file
>          You might need to add atom HB to the hydrogen database of 
> building block HEME
>          in the file aminoacids.hdb (see the manual)
>
>
> WARNING: atom HC is missing in residue HEM 513 in the pdb file
>          You might need to add atom HC to the hydrogen database of 
> building block HEME
>          in the file aminoacids.hdb (see the manual)
>
> .
> .
> .
> .
> .
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.5.3
> Source code file: pdb2top.c, line: 1449
>
> Fatal error:
> There were 30 missing atoms in molecule Protein, if you want to use 
> this incomplete topology anyhow, use the option -missing
> For more information and tips for troubleshooting, please check the 
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> Can anyone help how can I generate and add hydrogen database 
> information for heme to be used with CHARMM27 ff?

You'll have to read the applicable sections of manual chapter 5, make a 
local copy of the charmm27.ff folder in your working directory and 
editing aminoacids.hdb to add the generation information. When you're 
done, please post your efforts so that others might be able to benefit 
from them in future. (Also, search first in case this has already happened!)

Mark
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