[gmx-users] heme group in protein

David van der Spoel spoel at xray.bmc.uu.se
Tue Apr 9 12:05:04 CEST 2002

On Tue, 9 Apr 2002, Maija Lahtela wrote:

>I am studying a protein containing heme group. I checked that heme is
>included ffgmx.rtp file and FE is ffgmx.atp. 
>Are there a topology file for heme available gromacs or should I generate
>it ( I got the error message in pdb2gmx that residue 'HEME' not found in
>residue topogy database).  I tried to make topology file for heme taken
>from pdb-file using PRODRG webserver but the error was that PRODRG does
>not model bond between non-carbon atoms.   
It must be the residue name, pdb2gmx should simply recognize it. Maybe you 
should rename it from 'HEME ' to ' HEME' or vice versa.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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