[gmx-users] about using amb2gmx.pl

[Mark Abraham]

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
http://wiki.gromacs.org/index.php/Coordinate_File#On_the_need_for_a_.gro_file
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!

Mark