Hi,
Your 'distance' command is calculating the center of mass of all atoms
in the first mask to the center of mass of all atoms in the second
mass, which is not what you want.
You could probably use the 'closest' command for this, just put the
ligand's name in place of solvent, e.g.
closest 1 .CA,C,O,N,H solventmask :SIA closestout closest.dat name SIA
See the manual for full command details. Let me know if this works for you.
-Dan
On Mon, May 6, 2024 at 9:47 AM Alexander Hung Lee via AMBER
<amber.ambermd.org> wrote:
>
> In my system, I have 45 copies of a ligand (all with resname SIA but with different resid's) floating around a receptor. I'm trying to track what's the closest distance between any of those ligands and the backbone. Is there something I'm missing? It seems to be tracking only one of the 45.
>
> Input:
> parm ../2_md/CPLX_Neut_Sol.parm7
> trajin ../2_md/10.1.produ.nc
> distance :SIA @CA,C,O,N,H out distance.txt
> run
>
> Ouput:
> #Frame Dis_00001
> 1 8.5270
> 2 8.5101
> 3 8.4704
> ...
> 138 13.1068
> 139 13.2145
> 140 13.5623
> 141 13.5264
>
> Alex Lee
> PhD Student
> Woods Research Group<https://woodsgroup.franklinresearch.uga.edu/>
> Department of Biochemistry & Molecular Biology
> Complex Carbohydrate Research Center
> University of Georgia
>
> 315 Riverbend Rd.
> Athens, GA 30602
> Email: ahl63010.uga.edu
> Mobile: (470) 641-3884
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Received on Mon May 06 2024 - 10:00:02 PDT
