[gmx-users] error in g_hbond

Justin A. Lemkul jalemkul at vt.edu
Sat Jul 12 15:11:24 CEST 2008

Biswaranjan Meher wrote:
> Dear GROMACS users,
> I am new to gmx-users.
> I am analysing the H-bonding in my trajectory with the tool g_hbond.
> The trajectory was generated by the AMBER force fields.
> Now I have converted the AMBER prmtop and inpcrd files to GROMACS .top 
> and .gro files.

How did you do this conversion?

> When I performed the g_hbond, I encountered with a fatal error

What was the command you issued?  Were you analyzing the .gro file, or some 
converted mdcrd file?

> Your computational box has shrunk too much.
> g_hbond can not handle this situation, sorry.
> Also I checked the postings in the archive related to this problem, but 
> I didnt get the solution completely.
> So is it a problem of my AMBER traj./pdb files I am using or it some 
> thing else.
> Can anyone will help me in this regard to get the solution ?

Use gmxcheck on whatever files you have tried to analyze to see if they contain 
the appropriate box vectors.  I don't know how you did the conversion of the 
files from AMBER --> GROMACS, so that's a possible source of error.


> Thanks in advance for your kind suggestions.
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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