Re: AMBER: Entropy calculations using NMODE

From: saurabh agrawal <imsam100.yahoo.co.in>
Date: Sat, 2 Feb 2008 19:20:13 +0530 (IST)
Hello,

Thanks for the reply.

I have Delta H = -4002 (calculated through MM-PBSA) and TSTOT = 502 (calculated through NMODE). Will the DeltaG (of binding) be -3500 or -4504?

I mean to ask TSTOT gives (-T delta S)  OR (T delta S). Which one is correct?  Because different  previous references are showing both the ways for NMODE results.

saurabh




--- On Sat, 2/2/08, Eddie Mende <pckboy.gmail.com> wrote:
From: Eddie Mende <pckboy@gmail.com>
Subject: Re: AMBER: Entropy calculations using NMODE
To: amber@scripps.edu
Date: Saturday, 2 February, 2008, 6:47 PM

Gut feeling tells me:

T > 0
delta S > 0

and there you go!

Sign must be positive or equal zero :)

But I wish I could see the output of your AMBER job

Regards

Edu
Graduate minion
saurabh agrawal wrote:
> Dear Amber Users,
>
> I have done Nmode calculations and found TSTOT values. But I am not
> able to understand the value I got through TSTOT is (-T deltaS) or (T
> deltaS) . In some previous references authors have used DeltaG (of
> binding) = Delta H - (TSTOT) and in some references it is DeltaG (of
> binding) = Delta H - (-TSTOT).
>
> Kindly reply me in this regard.
>
> Thanking you in advance.
>
> saurabh
>
>
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Unlimited freedom, unlimited storage. Get it now ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu Received on Sun Feb 03 2008 - 06:07:38 PST
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