[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.
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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