Hello,
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
Regards,
Nikhil
________________________________
From: Mark Abraham <[email protected]>
To: Discussion list for GROMACS users <[email protected]>
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.
Mark
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