[gmx-users] Coordinate file does not match topology

David van der Spoel spoel at xray.bmc.uu.se
Sun Jun 10 22:27:09 CEST 2007

Sheyore Omovie wrote:
> Thanks Yang,
> Each of the residues in my *.gro have more H-atoms than in *.top. I 
> added the 21 H-atoms in [molecules] section of *.top. But grompp still 
> came up with the ff error: No such molecule type.
> Do i have to edit [moleculetype] section too?
> Rgds
> John

Please do not edit the topology file unless you are very sure what you 
are doing. You probably select a united atom force field and want to 
combine it with an all atom coordinate file. You will have to use the 
conf.gro that pdb2gmx produces.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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