Hello,<br><br>For usual peptides having amino acids you need not use Dundee Prodrg server.<br>pdb2gmx itself will generate the required .itp and .gro files.<br>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.<br>
May be this explanation will help.<br><br>Regards,<br>Pawan<br><br><div class="gmail_quote">On Thu, Apr 9, 2009 at 10:17 AM, Bhawana Gupta <span dir="ltr"><<a href="mailto:bhawana.gupta2010@gmail.com">bhawana.gupta2010@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div>Hello sir,</div>
<div> </div>
<div>From last few days , i was using TINKER for implicit simulations using force field oplsaa</div>
<div>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.</div>
<div> </div>
<div>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.</div>
<div> </div>
<div>Tell me what to do.</div>
<div> </div>
<div>Can i switch to gromacs older version i.e.3.3.1???</div>
<div> </div>
<div>Whether i can use The Dundee Prodrg server for peptides having usual amino acid???</div>
<div> </div>
<div>With regards,</div>
<div>Bhawana</div>
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