[gmx-users] H-Db error

Mark Abraham Mark.Abraham at anu.edu.au
Sun Jul 19 11:13:05 CEST 2009

nikhil damle wrote:
> Hi,
> I added peptide H to the the new residue i added to .rtp file in the ffG43a1.hdb file But the pdb2gmx gives error saying it can not read hdb file. If i remove this H from .hdb file, it gives error of missing atom. How should i resolve this problem ? y can pdb2gmx not read hdb file if i add one extra H ??

If your version of the .hdb file can't be read, then you've broken the 
format (see chapter 5), or created a file that does not adhere to the 
right conventions (e.g. by having Windows-style line endings - fix using 
dos2unix utility), or mangled the file permissions, or quite a few other 


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