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