[gmx-users] special molecule
Mark.Abraham at anu.edu.au
Mon Jun 12 17:16:23 CEST 2006
Tamas Horvath wrote:
> As I understand, if there are "special" molecules in a pdb file, pdb2gmx
> cannot convert it. However, PRODRG can create an *.itp file for that
> molecule, so that I can include it in the generated topology file. But
> how can I place the molecule in it's original position? Or even better,
> how can I convert the original ("full") .pdb file for gromacs?
Where's the problem? pdb2gmx makes a .top file for your non-special
system, you #include the .itp file for your special part. There's
nothing about atomic positions yet.... have a look at a .top file. Now
grompp takes the .top and some file with atomic positions and makes a
.tpr file. Same general procedure as normal.
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