[gmx-users] error in converting charmm to gromacs !!

Mark Abraham Mark.Abraham at anu.edu.au
Wed Sep 30 07:03:01 CEST 2009

Chanchal wrote:
> Hi All/Justin,
>    I got the *.atp file from Mark Abraham and now it is not complaining 
> about ON2b atom type. But now I am getting the following error while I 
> was trying to create *.top file using the command: 
> /Users/parimalkar/gromacs-4.0.5/bin/pdb2gmx_d -ff charmm -f 
> step5_assembly.pdb -p topol.top -o dopc.pdb
> Program pdb2gmx_d, VERSION 4.0.5
> Source code file: ter_db.c, line: 87
> Fatal error:
> Reading Termini Database: expected 3 items of atom data in stead of 1 on 
> line
>        N      NH3        14.0027    -0.3000
> -------------------------------------------------------

The format of the .tdb has changed over time. Try the one in GROMACS 
4.0.5 rather than Yuguang's.

Do you *really* need to use CHARMM? :-) Some other force field would be 
a much better idea until you're experienced enough to cope with solving 
these problems yourself.


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