Re: [AMBER] Distance between residues: Too many iteration in routine

From: He, Amy via AMBER <amber.ambermd.org>
Date: Thu, 2 Mar 2023 18:29:28 +0000

Hi,

“geom” returns the center of mass (default) of specified atoms – these could be residues if you specify residues, if my understanding is correct.

Are you possibly only interested in the sidechain? Or a certain portion on each residue? In that case you can refine your mask to narrow down the selection of atoms.

From: Hocine EL KHAOUDI ENYOURY <hocine.el-khaoudi-enyoury.etu.unistra.fr>
Date: Thursday, March 2, 2023 at 1:27 PM
To: AMBER Mailing List <amber.ambermd.org>, He, Amy <he.1768.buckeyemail.osu.edu>
Subject: Re: [AMBER] Distance between residues: Too many iteration in routine
Hi, I’ve tried with geom, but it seems that for atoms and not for residues. Bests Hocine Le 2 mars 2023 à 19: 23 +0100, He, Amy <he. 1768@ buckeyemail. osu. edu>, a écrit : Hi, The “geom” option of the “distance” command allows you

Hi,

I’ve tried with geom, but it seems that for atoms and not for residues.

Bests

Hocine
Le 2 mars 2023 à 19:23 +0100, He, Amy <he.1768.buckeyemail.osu.edu>, a écrit :

Hi,

The “geom” option of the “distance” command allows you to use the geometric centers.
https://amberhub.chpc.utah.edu/distance/<https://urldefense.com/v3/__https:/amberhub.chpc.utah.edu/distance/__;!!KGKeukY!yes0llRDYWyIsGN9F-zjL9nIl6lAomK_YsS0Aa-LSR45hfn1cSFYbEbNtLEjOAuVp19IkvkcJZvfUGqVEbp6v66Vp5FPyI5yR6Rr7saGNLla$>

Bests,
Amy 


--
Amy He
Chemistry Graduate Teaching Assistant
Hadad Research Group
Ohio State University
he.1768.osu.edu<mailto:he.1768.osu.edu>
From: Hocine EL KHAOUDI ENYOURY via AMBER <amber.ambermd.org>
Date: Thursday, March 2, 2023 at 1:20 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] Distance between residues: Too many iteration in routine
Dear amber community,
I’m trying to determine the distance between 2 residues over time with the following script.
parm protein.psf
trajin protein.dcd
rms first fit .CA
distance abc :4 :19 out distance.dat noimage
Is there any way to define a centre of mass for both residues and track the distance, without having to do it with atoms?
Thanks in advance!
Hocine
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Received on Thu Mar 02 2023 - 11:00:02 PST
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