[gmx-users] heme group in protein

Michel Fodje michel.fodje at mbfys.lu.se
Tue Apr 9 13:37:10 CEST 2002

I've had a few of these problems  especially with atoms or residues that
have too long names not supported by PDB but present in gromacs

One thing that works for me is

editconf -f file.pdb -o file.gro

Then edit file.gro and change the names to what ever you like, then use
file.gro as input for pdb2gmx


On Tue, 2002-04-09 at 12:43, David van der Spoel wrote:
    On Tue, 9 Apr 2002, Maija Lahtela wrote:
    >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.    
    What I meant is that spacing is important. You may have to shift the HEME 
    residue name a character to the left or to the right.
    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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Michel N. Fodje
Molecular Biophysics,
Lund University, Sweden

phone: +46 46 222 45 13
email: michel.fodje at mbfys.lu.se
web:   http://www.mbfys.lu.se

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