Re: [AMBER] Loading Topology & Trajectory Files

From: Daniel Roe <>
Date: Mon, 22 Mar 2021 10:37:49 -0400


You can do all the analysis in one script. However, be aware that
certain analyses (like 'rms' with fitting) will alter the coordinates
for subsequent analyses. This is in general more important for older
versions of cpptraj (< 5.0) but is important to be aware of in all

Below is an example of having everything done in one pass, where the
commands that do not modify coordinates come first. I'm taking
advantage of the fact that you typically want to fit coordinates to a
reference structure for 'rmsf' to remove global rotation/translation
anyway (which is why 'rmsf' comes after 'rms'); here I'm using the
first frame as a reference but you may want to use something else.
Also note I'm just doing the 'bare-bones' versions of these commands;
you'll want to check the manual for full details (particularly for a
more complex command like 'hbond'). Replace <mask> with masks
selecting your desired atoms. If you want a better surface area than
LCPO, replace 'surf' with 'molsurf' (but be aware it is slower). RoG,
HB, LCPO, ToFirst, and Fluct are just used to name the resulting data
sets and can be changed to whatever you like. Hope this helps.

parm topology.parm7
# Actions that do not modify coordinates
rog RoG <mask> out rog.dat
hbond HB <mask> out nhbonds.dat avgout hbavg.dat
surf LCPO <mask> out
# Best-fit RMSD performed by default
rmsd ToFirst first <mask> out rmsd.tofirst.dat
rmsf Fluct <mask> out rmsf.dat

Hope this helps,


PS - You may find the analysis tutorials helpful:

On Fri, Mar 19, 2021 at 5:25 PM Jatin Kashyap <> wrote:
> Dear AMBER Community,
> I have question about CPPTRAJ. I have to perform RMSD, RMSF, HBOND, SASA,& RoG analysis on around 20 complexes through a shell script based batch job.
> For a given complex, do I have to load topology & trajectory file for all of the individual analysis separately or I can just load it once and then perform RMSD, RMSF, HBOND, SASA, & RoG analysis one by one?
> Thank you.
> ——
> Jatin Kashyap
> Ph.D. Student
> Dr. Dibakar Datta Group
> Department of Mechanical and Industrial Engineering
> New Jersey Institute of Technology (NJIT)
> University Heights
> Newark, NJ 07102-1982
> Phone- (201)889-5783
> Email-
> _______________________________________________
> AMBER mailing list

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Received on Mon Mar 22 2021 - 08:00:02 PDT
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