[gmx-users] pdb file and force filed
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.
> 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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