[gmx-users] centroid distance for tyrosine

[Archana Sonawani-Jagtap]

sorry I didn't understood the syntax in first go, I was getting errors as I
missed the single quotes but now it worked.

gmx distance -f apo-cxcr4-final1.xtc -s mdmodified_cxcr4.tpr -n
nter_index.ndx -select 'cog of group "7Y_cog"  plus cog of group "12Y_cog"'

Thanks


On Sun, Feb 17, 2019 at 12:37 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/16/19 2:01 PM, Archana Sonawani-Jagtap wrote:
> > Hi Justin,
> >
> > I think something is wrong in the command because when I visualize the
> > distance between OH atoms of tyrosine's in VMD it shows ranging from 3 to
> > 10 ang. Also, when I take single frame in pdb format and check centroid
> > distance using PIC webserver, it gives within same range. However, using
> > above command it gives distance within 1.37-1.38 ang.
> >
> > I used following command:
> >
> > gmx distance -f apo-cxcr4-final1.xtc -s mdmodified_cxcr4.tpr -n
> > nter_index.ndx -oav distave_tyr12-21.xvg -select 12Y_cog  21Y_cog -oall
> > dist_tyr12-21.xvg
> >
> > What could be wrong?
>
> You didn't use the syntax I gave you (and I'm not sure how what you
> provided is even a valid command).
>
> gmx distance is giving you what you asked for, all distances (-oall) in
> the groups provided, so you're seeing values that are consistent with
> C-C bond lengths.
>
> -Justin
>
> >
> >
> >
> >
> > On Sat, Feb 16, 2019 at 4:31 AM Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >>
> >> On 2/15/19 2:37 PM, Archana Sonawani-Jagtap wrote:
> >>> Hi,
> >>>
> >>> I want to calculate centroid distance between 2 tyrosine rings
> throughout
> >>> the simulation. Which option of gmx distance can help to plot the
> >> centroid
> >>> distance?
> >> Create two index groups with the ring atoms, then use gmx distance:
> >>
> >> gmx distance -s -f -select 'cog of group "ring1" plus cog of group
> "ring2"'
> >>
> >> -Justin
> >>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Office: 301 Fralin Hall
> >> Lab: 303 Engel Hall
> >>
> >> Virginia Tech Department of Biochemistry
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalemkul at vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==================================================
> >>
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
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