[gmx-users] problem with pdm2gmx

[Anton Feenstra]

jozef hritz wrote:
> 
>         Dear Hugo,
> 
> > I have used the PRODRG server to convert a molecule. The minimization in gromacs
> > works fine. But when I tried to run pdb2gmx to make a .pdb file and see it in
> > VMD, I received the following error:
> 
> For creation of .pdb file You can use editconf.

Right. pdb2gmx is the Gromacs automated topology builder which works
only for recognized building blocks (e.g. amino acids). So it doesn't
make much sense to use pdb2gmx if you already have the topology (that
PRODRG did for you...).

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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