[gmx-users] pdb file and force filed

Pawan Kumar pawan.chinari at gmail.com
Thu Apr 9 06:58:41 CEST 2009


For usual peptides having amino acids you need not use Dundee Prodrg server.
pdb2gmx itself will generate the required .itp and .gro files.
If u were using opls force fiels in tinker then use the same force fields in
gromacs also because atom types are defined in different ways in different
force fields.
May be this explanation will help.


On Thu, Apr 9, 2009 at 10:17 AM, Bhawana Gupta
<bhawana.gupta2010 at gmail.com>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.
> 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???
> With regards,
> Bhawana
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