[gmx-users] Question Re. KALP-15 in DPPC tutorial

[Justin Lemkul]

On 1/24/14, 11:21 PM, jhosamelly wrote:
>
> Thanks Justin. I fixed the problem earlier but when I got to
>
> "2. Pack the lipids around the protein
>
> The easiest method I have found so far for packing lipids around an embedded
> protein is the InflateGRO methodology (ref), available here. First,
> concatenate the protein and bilayer structure files:
>
> cat KALP_newbox.gro dppc128_whole.gro > system.gro
>
> Remove unnecessary lines (the box vectors from the KALP structure, the
> header information from the DPPC structure) and update the second line of
> the coordinate file (total number of atoms) accordingly."
>
> I don't know what file to edit. Remove unnecessary lines in what file?

In system.gro.  If you study the file format and examine what you have created, 
you will see that there is extraneous stuff that will break the file format.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
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Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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