Re: [AMBER] lipidscd S.D.

From: Stephan Schott <>
Date: Mon, 28 Jan 2019 18:26:24 +0100

Thanks for the heads up.

The first is that 'lipidorder' cannot distinguish between the two OL tails
> of each
> lipid, so the results are for all OL residues, whereas 'lipidscd' does
> results for each separate tail.

 I was aware of the calculation difference, but if that would have been the
relevant difference, the error in lipidorder should have been higher, as
the average goes over sn1 and sn2 tails, and not the other way around.

In your system there are also
> different linkers for some lipids - I may need to update 'lipidscd' to
> distinguish based on this as well.

A "perhead" flag would be cool :O

> The second difference is in how the standard deviations are
> calculated. In 'lipidorder', the standard devation is for the averaged
> SCD values, whereas for 'lipidscd' the standard devation is for all
> individual SCD values. The averages work out to be the same, but this
> is why the magnitude of the current 'lipidscd' s.d. values are much
> larger than for 'lipidorder'. I'm pretty sure that what people want
> typically is what 'lipidorder' reports (i.e. for a single frame the
> s.d. for each position should be zero.). This also explains the
> unexpected behavior of 'lipidscd' s.d. values that was reported
> eariler.

Thanks for looking into it!


Stephan Schott Verdugo
Heinrich-Heine-Universitaet Duesseldorf
Institut fuer Pharm. und Med. Chemie
Universitaetsstr. 1
40225 Duesseldorf
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Received on Mon Jan 28 2019 - 09:30:02 PST
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