<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
This still does not work.<br>
<br>
I source the gromacs tree with GMXRC first. Then I set the GMXLIB to
the share/gromacs/top/. I have a custom ffgmx2.hdb (which works fine
in 4.0.7) in my working directory to protonate united atom
trajectories of lipid bilayer simulations. So this is what I have:<br>
<br>
$ echo $GMXLIB<br>
/Volumes/gravensteiner/install/gromacs4.5.2/share/gromacs/top/<br>
$ which g_protonate<br>
/Volumes/gravensteiner/install/gromacs4.5.2/bin/g_protonate<br>
<br>
And the error is exactly this:<br>
<br>
Program g_protonate, VERSION 4.5.2<br>
Source code file: futil.c, line: 891<br>
<br>
Fatal error:<br>
Library file ffgmx2 not found in current dir nor in your GMXLIB
path.<br>
<br>
And it stops, doing nothing. I get the same with version 4.5.3.<br>
<br>
I'm open to more suggestions! :)<br>
<br>
Regards<br>
Jon<br>
<br>
<br>
<br>
On 12/10/2010 12:52 PM, Sarath Chandra wrote:
<blockquote
cite="mid:AANLkTinyvTuTysZbP3cCJZc08W3e7E1AQB2O-TAuJUMa@mail.gmail.com"
type="cite"><br>
<br>
<div class="gmail_quote">On Fri, Dec 10, 2010 at 12:41 PM, Jon
Kapla <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:jon.kapla@mmk.su.se" target="_blank">jon.kapla@mmk.su.se</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Thank you for the answer<br>
<br>
Does this mean that if I want to use a custom .hdb-file in the
working directory it should be named aminoacids.hdb?<br>
Shouldn't GMXLIB be set when sourcing bin/GMXRC by the way? It
seems to be empty after sourcing on both my machines.<br>
Not a big problem though.<br>
<br>
</blockquote>
<div><br>
You dont have to rename anything. You can either add the
following line to your .bashrc (if using bash)<br>
<br>
export GMXLIB="/usr/local/gromacs/45x/share/gromacs/top"<br>
<br>
<br>
or run the same command on your terminal<br>
<br>
<br>
Best Wishes,<br>
<br>
Sarath<br>
<br>
</div>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Regards<br>
<font color="#888888">
Jon</font>
<div>
<div><br>
<br>
</div>
</div>
</blockquote>
<div><br>
<br>
</div>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div>
<div>
<br>
On 12/10/2010 12:30 PM, Sarath Chandra wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<br>
In Gromacs4.5.x the structure of the top directory has
changed. The path for .hdb file is in gmx2.ff and under
the name aminoacids.hdb<br>
<br>
Changing your GMXLIB would solve the problem...<br>
<br>
for eg: /usr/local/gromacs/45x/share/gromacs/top<br>
<br>
--<br>
<br>
Sarath<br>
</blockquote>
</div>
</div>
</blockquote>
</div>
<br>
</blockquote>
<br>
</body>
</html>