[gmx-users] problem with charmm

Justin A. Lemkul jalemkul at vt.edu
Mon Jul 21 16:39:04 CEST 2008

sarbani chattopadhyay wrote:
>   hi,
>     I have followed the process as told by Yuguan Mu.But while using the 
> comman "pdb2gmax"
> I get the following error
> Source code file: ter_db.c, line: 85
> Fatal error:
> Reading Termini Database: expected 3 items of atom data in stead of 1 on 
> line
>       N      NH3        14.0027    -0.3000
> I am not being able to fix this problem.

Well, what have you tried?  If you want free help, you'll have to demonstrate 
that you're resourceful :)

Read in the manual about file formats.  The files that are available online for 
download are designed for an older version of Gromacs (3.1.x?), and there have 
been some changes to the file format since then.  You will have to edit the .tdb 
files, at the very least.


> Thanks in advance
> Sarbani
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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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