[gmx-users] about using amb2gmx.pl

Mark Abraham Mark.Abraham at anu.edu.au
Sat Feb 16 13:54:22 CET 2008

xi zhao wrote:
> Dear all users:
> I want to simulate a system ( protein + chromophore). I 
> have had chromophore.gro and its top file using amb2gmx.pl,but I find I 
> can not use them to translate PDB( protein + chromophore) file into gro 
> and top files properly. So  I need your advice about further procedure!
> Thank you very much   

You don't need a .gro file. See
The grompp utility will happily make a .tpr from your .mdp, your .top
file, and your well-formed .pdb file whose atom, residue and molecule
names and ordering matches the .top file. This last constraint also
applies to a .gro file!


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