<html>
<head>
<style><!--
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Tahoma
}
--></style>
</head>
<body class='hmmessage'>
<br><br>> If you simple replace HETATM with ATOM, i.e.:<br>> <br>> :1,$s/HETATM/ATOM/<br>> <br>> you shift all columns left by two characters. This is probably why, instead of <br>> reading GLY, pdb2gmx is reading Y only. The proper replacement would be:<br>> <br>> :1,$s/HETATM/ATOM /<br>> <br>> Note the two trailing spaces after ATOM.<br>> <br>> -Justin<br><br>Justin, adding the two spaces did the job. Thanks<br>                                            </body>
</html>