[gmx-users] centering a protofibril in a box

Justin Lemkul jalemkul at vt.edu
Thu Nov 6 23:54:20 CET 2014

On 11/6/14 10:58 AM, Adriana Garro wrote:
> Thanks Justin.
> I know it was not enough clear, it was because of my limited English
> proficiency.
> What I wanted (and want) to do is centering the first monomer of the
> protofibril in the box, so the protofibril would be shifted to the bottom
> part allowing aggregate more and more monomers without having to use a
> bigger box.
> But using this
> trjconv -f protofibril.pdb -n index.ndx -center -s  protofibril.pdb -o
> test.pdb
> (index.ndx  is an index I did for the residues corresponding to the first
> monomer and that is which I chose as "select group for centering")
> what I get is that the center of the box matches with the center of the
> protofibril (looking at the longitudinal direction of the protofibril), as
> it doesnt care about the index.

I suppose it depends on the dimensions of the box as defined in the .pdb file.

> By the way, do you know why  -s file.pdb is required?

In general, it depends on what you're actually doing.  The information in -s may 
be used for box information, masses, atom/residue names, etc.  In this case, 
trjconv needs names.  Any time you want to write a coordinate file, you need to 
supply a suitable input for -s.

> Maybe it is not possible to do what I want with this command; but it is
> just center the protofibril with respect to its first monomer.
> I will try with editconf instead.

That would likely be easiest.  Extract the COM coordinates using g_traj, then 
you know exactly how much you need to translate the structure.



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


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