[gmx-users] pdb file and force filed

Mark Abraham Mark.Abraham at anu.edu.au
Thu Apr 9 07:04:55 CEST 2009

Bhawana Gupta wrote:
> Hello sir,
>  From last few days , i was using TINKER for implicit simulations using 
> force field oplsaa
> Now for explicit one, i switched to gromacs version 4.0.But if i take 
> pdb file from tinker (molecular modelling software) and paste it in The 
> Dundee Prodrg server. i got my *.itp file, *.gro file.

This server generates a topology that is possibly suitable for use with 
one specific force field.

> But if i use force field as ffoplsaa or ffG43a1 or any other force field 
> except ffgmx. I always got error in atom type not found.

As expected.

> Tell me what to do.
> Can i switch to gromacs older version i.e.3.3.1???


> Whether i can use The Dundee Prodrg server for peptides having usual 
> amino acid???

You can, but pdb2gmx will give a wider choice of force field with more 
reliable parameters - for the usual residues.


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