[gmx-users] H-Db error

nikhil damle pdnikhil at yahoo.co.in
Sun Jul 19 11:21:21 CEST 2009

Thanks for the reply. I am trying to add N-H hydrogen of a residue which is tab separated formate; just like other residues. if i remove this H from .hdb file, file can be read and pdb2gmx gives missing atom error. But when i have it in the file, it can not read it. if there were version related problem, it should give same error even after removing this H. i m using Gromacs-4.0.5 on linux machine. so no OS related problems possible


From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Sunday, 19 July, 2009 2:43:05 PM
Subject: Re: [gmx-users] H-Db error

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 possiblities.

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