[gmx-users] how to create topology file for butane

Mark Abraham Mark.Abraham at anu.edu.au
Fri Aug 21 16:40:42 CEST 2009

simon sangma wrote:
> Respected sir,                         I am working on GROMACS. I need your
> help.I am trying to generate topology file for non-standard molecules like
> butane, water. I am executing following command.
> *pdb2gmx -f ALA.pdb -p ALA.top -o ALA.gro*
> **
> It is successfully working on amino acid residue.
> But when i am executing it for butane.
> *pdb2gmx -f BUTANE.pdb -p BUTANE.top -o BUTANE.gro*
> **
> **
> Fatal error:
> Residue 'DRG' not found in residue topology database

That's normal - pdb2gmx can only build topologies for types of molecules 
present in its .rtp file database. Depending on the force field, that 
might be only proteins.

There are some helper programs out there (PRODRG, x2top, topolbuild, 
probably others) but they tend to be force-field specific. For butane, 
you should probably have a good read of chapter 5 of the manual, and 
write one by hand. Use a peptide .top as a template.


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