[gmx-users] heme group in protein

Maija Lahtela mlahtela at csc.fi
Tue Apr 9 09:36:09 CEST 2002


I tried this by changing the pdb file name HEM to HEME before I run
pdb2gmx without luck.  pdb2gmx is not recognizing the heme group.    

Maija L-K

> >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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Maija Lahtela-Kakkonen, 
Research Scientist
Department of Pharmaceutical Chemistry
University of Kuopio
P.O.Box 1627, FIN-70210 Kuopio, FINLAND
tel: +358-(0)17-162462, fax:+358-(0)17-162456
e-mail: mlahtela at csc.fi

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