[gmx-users] pdb2gmx + non-protein

[K.A. Feenstra]

David wrote:
> On Thu, 2003-01-30 at 20:27, Alberto Imparato wrote:
> 
>>Hi All
>>I'm trying to obtain a topology file starting from a very simple .gro
>>file, using pdb2gmx .
>>My 2_dppc.gro file contains 2 DPPC molecules, each containing 50 atoms:
[...]
>>WHY the 2 molecules are not recognized as DPPC molecules, but are treated
>>as 1 single Protein ???
> 
> pdb2gmx only works for residue types that are present in the database.
> DPPC is not. Check Peter Tieleman's website.

It must actually be in the database, else pdb2gmx would not generate output.
The name 'protein' in your .top file is nothing more than a label, in this
case it actually refers to a topology of your dppc molecules. pdb2gmx cannot
know this.

But, you probably do not want to use a topology like this. You'd better follow
the way Peter Tieleman did it.

Perhaps it is good to stress this once again: pdb2gmx was designed to build
a *protein* topology from residues. It also happens to work for DNA and some
other polymeric systems. Additionally, the database contains some separate
molecules, which will be treated as yet another residue. But it doesn't
really make sense to use pdb2gmx for that. If you have .itp files for your
separate molecules (like spc.itp for water, dppc.itp for DPPC), you can
write a very short .top file which includes the forcefield parameters, and
the topology definition of your molecules, and the definition of your
system.


-- 
Groetjes,

Anton
  ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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