AMBER Archive (2009)

Subject: [AMBER] PRINCIPAL QUESTION

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Dear all,

as I reported sooner (in "SOS - too high binding energy" email) I have
problem
with nice complex (please see the attachment) for which I surprisingly
calculated
positive mean value of binding energy (20,86 kcal/mol). Here is the
statistic for One trajectory approach.

ONE TRAJECTORY APPROACH
                        
dH - mean value -53,67
dH - standard deviation 13,11
TdS - mean value -74,53
TdS - standard deviation 9,05
dG = dH - TdS - mean value 20,86
dG = dH - TdS - standard deviation 15,93030445

I have just simple but principal question.

It is THEORETICALLY possible stable complex where favourable decreas in
enthalpy after binding is more than compensate
by entropy penalty because of the unfavourable loss in entropy after
complexation ?.

Thank you very much in advance for any comment or relevant article/(www
link) redirection.

With the best regards

   Marek

-- 
Tato zpráva byla vytvoøena pøevratným po¹tovním klientem Opery:  
http://www.opera.com/mail/

• image/png attachment: B_malt_ssDNA_11ns.png

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• Previous message: Ross Walker: "RE: [AMBER] ptraj "image" "center" commands"
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