[gmx-users] g_energy -fee -inf problem

[Naser, Md Abu]

Hi Mark,

The reacton shuld occur as: R-S-S-R + 2H+ -----> 2R-SH.

With regards,

Abu Naser 

School Of Life Sciences 
Heriot-Watt University 
Edinburgh EH14 4AS 
Email: mn2 at hw.ac.uk
Phone: +44(0)1314518265 
Fax : +44(0) 131 451 3009 


 



-----Original Message-----
From: gmx-users-bounces at gromacs.org on behalf of Mark Abraham
Sent: Mon 24/09/2007 9:02 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_energy -fee -inf problem
 
Naser, Md Abu wrote:
> Hi Mark,
> 
> Thank you very much for your replay.I was just trying to
> calculate free energy difference between reduced protein and non-reduced
> protein solvated in water(spc) using ffG43a2 force field.

OK, so other than bond cleavage, what happens to the sulfurs when you 
reduce them in a real system?

Mark

> -----Original Message-----
> From: gmx-users-bounces at gromacs.org on behalf of Mark Abraham
> Sent: Sat 22/09/2007 6:05 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] g_energy -fee -inf problem
> 
> Naser, Md Abu wrote:
>  > Hi All User,
>  >
>  > I am getting free energy difference -inf.
>  > 1st I run a protein in water molecule and then I made a different
>  > topology file with deleting 4 disulfide bonds and accordingly the 
> angles and
>  > diherdal angles.
> 
> What physical model are you trying to reproduce here?
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