[gmx-users] H-atoms in .hdb file

Justin A. Lemkul jalemkul at vt.edu
Tue Jun 26 17:50:07 CEST 2012

On 6/26/12 11:47 AM, Shima Arasteh wrote:
> OK, but when I chose none, it gives me a fatal error ( dangling bond! ). A new problem! So how do I solve it?

"Dangling bond" errors were introduced as part of the output in Gromacs 4.5. 
The "aminoacids.dat" file was only used by older (4.0.x and earlier) versions of 
Gromacs.  You need to be modifying "residuetypes.dat" to indicate that FOR is a 
Protein residue so that the chain is continuous with respect to its content type.




Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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