[gmx-users] heme group in protein

[Michel Fodje]

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
topologies.

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

Michel


On Tue, 2002-04-09 at 12:43, David van der Spoel wrote:
    On Tue, 9 Apr 2002, Maija Lahtela wrote:
    
    >Hi,
    >
    >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
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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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