[gmx-users] centering a protofibril in a box

[Tsjerk Wassenaar]

Hi Adriana,

Centering only shifts the positions. I guess you also want to put stuff
back into the box and then make the molecules whole. You'll probably need
several passes to get what you want.

Cheers,

Tsjerk
On Nov 6, 2014 11:54 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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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