[gmx-users] centering a protofibril in a box

Adriana Garro adrianagarrosl at gmail.com
Thu Nov 6 16:58:05 CET 2014

Thanks Justin.
I know it was not enough clear, it was because of my limited English
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

(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.
By the way, do you know why  -s file.pdb is required?
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.
Thanks a lot for your time.


Dra. Adriana D. Garro
Química Medicinal
Facultad de Química, Bioquímica y Farmacia
Universidad Nacional de San Luis
San Luis, Argentina

Tel..............:+54 266 4424689  int 6153
e-mail...: adgarro at unsl.edu.ar
e-mail...:  adrianagarrosl at gmail.com


2014-11-06 13:54 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:

> On 11/6/14 6:13 AM, Adriana Garro wrote:
>> Dear all,
>> I am trying to center a protofibril in a box, but respect to its first
>> monomer. (the result would be the protofibril shiftted to the botton of
>> the
>> box)
>> I used
>> trjconv -f protofibril.pdb -n index.ndx -center -s  protofibril.pdb -o
>> test.pdb
>> I did an index for the residues corresponding to the first monomer and
>> that
>> is which I chose as "select group for centering" but when I visualize the
>> System with vmd the protofibril appears in the center of the box but as it
>> was just one molecule.
> You can accomplish this with either editconf -translate or trjconv
> -trans.  I don't exactly know what's going on from your description - an
> image here would be good, because the last sentence doesn't make much sense
> to me.
> -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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