[gmx-users] KALP15 in DPPC Analysis section

[Justin Lemkul]

On 10/27/16 2:18 PM, Sailesh Bataju wrote:
> Hi,
>
> I've been following KAlP15 in DPPC tutorial successfully but now I stuck in
> the last Analysis section. I googled the problem there's nothing out. The
> question is so simple it's just a misunderstanding. In the 2nd part Density
> of the Membrane the code is
>
> # gmx make_ndx -f md_0_1.tpr -o density_groups.ndx
> ...
>  > 12 & a C1 | a C2 | a C3 | a N4 | ... | a O11
>  > name 22 Headgroups
>  > 12 & a C12 | a C13 | a O14 | ... | a C50
>  > name 23 Tails
>  > q
>
> I don't get what should I've to put in place of "..." . It's so confusing.
> In 1st line after aN4, should I continue from "a N5 to a N10" or  "a O0 to
> a O10"?
>
> Similarly, in 3rd line after a O14, should I continue from "a O15 to a O49"
> or "a C15 to a C49"?
>
> Or, N and O are just typo, instead C should be placed?
>

The atom names are right.  Look at the coordinate file, and label the atoms 
using visualization software if you need to.  It's pretty standard lipid 
nomenclature.

The ellipsis (...) means "I've already typed up this whole tutorial and now I'm 
tired of typing all of this, so you fill in the blank here with the necessary 
atom names."  This implies that you have already familiarized yourself with what 
atom names constitute the lipid headgroup (note that I've stopped at O11, which 
means that's the end of the headgroup) and the tails (which start from C12).

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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