[gmx-users] How to get the all atom topology file for smallmolecule?

Peter Zoon zoon at science.uva.nl
Fri Jan 23 09:52:01 CET 2004

>Hi Yuhua
>I need to build a topology manualy and it was a hard work, but after 
>you do the first one you will see that the work is not so hard.
>You can look at file ffoplsaa.atp and find the atom types that are 
>better for your molecule. After this, you can add a new fragment in 
>ffoplsaa.rpt with this atom types you choose. Now you can use a pdb 
>file of your molecule with pdb2gmx and get your topology.

But doesn't pdb2gmx only work is there are valid amino-acid residue 
types specified in your pdb-file? If this is a small drug molecule I 
can imagine that it isn't made from amino-acids.

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