[RASMB] Vbar for a peptide

Laue, Thomas Tom.Laue at unh.edu
Wed May 9 08:10:13 PDT 2018


The reference is in help file for Sednterp.
I believe the calculations you are doing do not incorporate the effects of the H-bonding, or there is some other problem in how the calculations are being done. Traube’s method for uncharged materials is accurate to within ~1%.
Tom

From: RASMB [mailto:rasmb-bounces at list.rasmb.org] On Behalf Of prasun kumar
Sent: Wednesday, May 9, 2018 11:08 AM
To: Rocco Mattia <mattia.rocco at hsanmartino.it>
Cc: rasmb at list.rasmb.org
Subject: Re: [RASMB] Vbar for a peptide

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That is great Rocco Mattia. Thank You very much. Can I have the reference for the formula.

Regards
Prasun

PRASUN (ASHOKA)
Desire + stability = Resolution
Resolution + Hard work = Success

On Wed, May 9, 2018 at 4:04 PM, Rocco Mattia <mattia.rocco at hsanmartino.it<mailto:mattia.rocco at hsanmartino.it>> wrote:

Sorry, I made a mistake in copying the equation for the T-dependence of vbar... the correct one is:


vbar(T °C) = vbar(25 °C) + [4.25 x 10-4 (T - T(25 °C))]



________________________________
Da: RASMB <rasmb-bounces at list.rasmb.org<mailto:rasmb-bounces at list.rasmb.org>> per conto di prasun kumar <prasun30 at gmail.com<mailto:prasun30 at gmail.com>>
Inviato: mercoledì 9 maggio 2018 16:25
A: rasmb at list.rasmb.org<mailto:rasmb at list.rasmb.org>
Oggetto: [RASMB] Vbar for a peptide

Hi Group:

I have gone through most of the discussions on Vbar and related stuff here. However, I thought to put my procedure for discussion...

I have a peptide that consist of 2 AiB residues alongwith other natural residues.
Since, the Vbar for AiB is not available, I was considering AiB as Ala and calculating the Vbar of the peptide. However, if Vbar goes down, it overestimates the Mol. Weight of the assembly. I was bit worried about this fact. Then I came across the paper by Durchschlag and Zipper in Jl of Appl. Cryst. (1997). In this paper authors have tried to calculate the partial specific volumes of small molecules and polymers based on volume increment method.

After going through the above article, I decided to randomize my sequence such that the constituent residues and their numbers remain same. I calculated the Vbar of both sequences and found no difference in Vbar at 20 C.

I also realized that 2 AiB residues can be replaced by one Ala and one Val. for example:
......AiB AiB........ can be ......AV.....

after replacing AiB AiB by AV, I calculated the Vbar of my peptide.

Here, it is important to note that I am not changing the charged or aromatic residues.
Any suggestion on the appropriateness of my procedure is welcome.

Regards
Prasun


PRASUN (ASHOKA)
Desire + stability = Resolution
Resolution + Hard work = Success
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