<html>
<head>
<style><!--
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Tahoma
}
--></style>
</head>
<body class='hmmessage'>
Dear gmx-users,<div><br></div><div>this seems like a trivial problem but has driven me crazy: </div><div><br></div><div>I have been trying to build a simple B-form dsDNA strand for use in MD simulations using Amber99sb. I have tried several platforms and each generates a pdb file which pdb2gmx cannot convert as it cannot understand the naming system of the other platforms.</div><div><br></div><div>Is there any platform that can be used to create DNA molecules with a naming system compatible with GROMACS, specifically with the Amber99sb ff?</div><div><br></div><div>Thanks</div><div><br></div><div>Will<br><br></div> </body>
</html>