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: [EMAIL PROTECTED] 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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