[RASMB] Vbar for a peptide

prasun kumar prasun30 at gmail.com
Wed May 9 08:15:13 PDT 2018


Thank You very much. I will have a look and continue with it.

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

On Wed, May 9, 2018 at 4:10 PM, Laue, Thomas <Tom.Laue at unh.edu> wrote:

> 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
>
>
>
> *Caution - External Email*
> ------------------------------
>
> 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>
> 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> per conto di prasun kumar <
> prasun30 at gmail.com>
> *Inviato:* mercoledì 9 maggio 2018 16:25
> *A:* 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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