<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
<title></title>
</head>
<body text="#000000" bgcolor="#ffffff">
On 12/02/2011 3:14 AM, william Stebbeds wrote:
<blockquote cite="mid:BLU118-W3F6F6571010086F795E96C1EF0@phx.gbl"
type="cite">
<style><!--
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Tahoma
}
--></style>
Hi Folks,<br>
<br>
I have added a custom DNA residue to the amber99sb ff, and
everything works perfectly, (thanks to Justin!).<br>
<br>
The residue is incorporated perfectly into the sequence, with no
abnormal events during simulations. I have updated all the files
to include the new residue.<br>
<br>
I have since realised, when using g_rms, that my custom residue is
not included in the default DNA index group, and appears as a
group on its own.<br>
<br>
Is there a way of making gromacs understand that this residue is
DNA when it makes the index files?<br>
<br>
I am not using make_ndx, I just let gromacs split the groups.<br>
<br>
Thanks in advance<br>
<br>
Will - Cranfield University<br>
</blockquote>
<br>
You need to arrange for the tools to access a modified form of
share/gromacs/top/residuetypes.dat with your custom residue suitably
classified. I understand you can copy that file to your working
directory and modify it there, and GROMACS will use the local copy.<br>
<br>
Mark<br>
</body>
</html>