<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
<HTML>
<HEAD>
<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
<META NAME="Generator" CONTENT="MS Exchange Server version 6.5.7652.24">
<TITLE>RE: [gmx-users] g_energy -fee -inf problem</TITLE>
</HEAD>
<BODY>
<!-- Converted from text/plain format -->
<P><FONT SIZE=2>Hi Mark,<BR>
<BR>
The reacton shuld occur as: R-S-S-R + 2H+ -----> 2R-SH.<BR>
<BR>
With regards,<BR>
<BR>
Abu Naser<BR>
<BR>
School Of Life Sciences<BR>
Heriot-Watt University<BR>
Edinburgh EH14 4AS<BR>
Email: mn2@hw.ac.uk<BR>
Phone: +44(0)1314518265<BR>
Fax : +44(0) 131 451 3009<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
-----Original Message-----<BR>
From: gmx-users-bounces@gromacs.org on behalf of Mark Abraham<BR>
Sent: Mon 24/09/2007 9:02 AM<BR>
To: Discussion list for GROMACS users<BR>
Subject: Re: [gmx-users] g_energy -fee -inf problem<BR>
<BR>
Naser, Md Abu wrote:<BR>
> Hi Mark,<BR>
><BR>
> Thank you very much for your replay.I was just trying to<BR>
> calculate free energy difference between reduced protein and non-reduced<BR>
> protein solvated in water(spc) using ffG43a2 force field.<BR>
<BR>
OK, so other than bond cleavage, what happens to the sulfurs when you<BR>
reduce them in a real system?<BR>
<BR>
Mark<BR>
<BR>
> -----Original Message-----<BR>
> From: gmx-users-bounces@gromacs.org on behalf of Mark Abraham<BR>
> Sent: Sat 22/09/2007 6:05 PM<BR>
> To: Discussion list for GROMACS users<BR>
> Subject: Re: [gmx-users] g_energy -fee -inf problem<BR>
><BR>
> Naser, Md Abu wrote:<BR>
> > Hi All User,<BR>
> ><BR>
> > I am getting free energy difference -inf.<BR>
> > 1st I run a protein in water molecule and then I made a different<BR>
> > topology file with deleting 4 disulfide bonds and accordingly the<BR>
> angles and<BR>
> > diherdal angles.<BR>
><BR>
> What physical model are you trying to reproduce here?<BR>
_______________________________________________<BR>
gmx-users mailing list gmx-users@gromacs.org<BR>
<A HREF="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>
Please search the archive at <A HREF="http://www.gromacs.org/search">http://www.gromacs.org/search</A> before posting!<BR>
Please don't post (un)subscribe requests to the list. Use the<BR>
www interface or send it to gmx-users-request@gromacs.org.<BR>
Can't post? Read <A HREF="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A><BR>
<BR>
</FONT>
</P>
</BODY>
</HTML>