[gmx-users] Residue 'HEM' not found in residue topology database

[Mark Abraham]

On 14/04/2011 5:59 PM, hui sun wrote:
> Dear all,
> I am having the troubles to obtain the topology file for Cytochrome 
> C.  When I used the Gromos96 53a6 force filed in the GROMACS 
> 4.0.7 software package, the topology file is produced, but there is 
> lack of some force field parameters, such as  the bonds from Cys 14 
> and Cys 17 to the porphyrin ring and to hold the ligands (Met 80 and 
> His 18) bound to the heme iron, in this file. When I used the Gromos96 
> 53a6 force filed in the GROMACS 4.5.1 software package, there's a 
> fatal error: Residue 'HEM' not found in residue topology database. I 
> have checked the rtp file, in which there is the "HEME" residue.
>

"HEM" will not always be considered the same as "HEME" by a computer 
algorithm... If they're meant to match, name them the same thing in each 
place.

Mark
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