Re: [AMBER] Remove motion of center of mass after obtaining trajectory

From: Daniel Roe <>
Date: Tue, 3 Jan 2017 09:06:17 -0500

On Sat, Dec 31, 2016 at 2:32 AM, The Cromicus Productions
<> wrote:
> I tried the following code in cpptraj, but it seems to not be doing
> anything. Any idea of what could I be doing incorrectly?

Not without more information - 'seems to not be doing anything'
doesn't give us a lot to go on. Can you at least provide the output
from cpptraj? I'll try to comment on your input below.

> parm dna-nowater.prmtop
> trajin md-nowater.mdcrd
> rms first :1-24&!.H=
> average crdset

It's not clear to me exactly what you wanted here since you're using
the 'crdset' keyword here as a file name (which in general you
shouldn't do). Make sure you read the manual entry for each command
carefully; 'average crdset' will create a file named 'crdset', while
'average crdset <set name>' will create a COORDS data set that you can
then use as a reference (and hence keep everything in memory).

> createcrd trajj1
> run
> reference crdset
> crdaction trajj1 rms ref crdset :1-24&!.H=

This seems ok (but pay attention to the output to make sure the
correct reference is being used etc). You're RMS-fitting the
coordinates in COORDS set 'traj1' to the reference 'crdset' (again, I
urge you *not* to use keywords as names since it's easy to get

> createcrd CRD1
> trajout 1.mdcrd mdcrd
> run

This is where you go wrong I suspect. You're specifying 'createcrd'
which is an Action, so it goes into the Action queue. Actions in the
Action queue operate on frames from input trajectories, which in this
case is 'md-nowater.mdcrd' - hence all you are doing is getting the
same trajectory back again. I suspect what you want is to output the
coordinates in the 'traj1' COORDS data set that you previously
RMS-fit. In this case you need to use the 'crdout' command instead of

crdout traj1 1.mdcrd

Hope this helps,


> On Fri, Dec 30, 2016 at 9:23 PM, The Cromicus Productions <
>> wrote:
>> Thanks! I'm currently playing with that
>> On Fri, Dec 30, 2016 at 4:21 PM, Hai Nguyen <> wrote:
>>> May be perform best fit RMSD to reference (starting) structure by cpptraj?
>>> Hai
>>> On Fri, Dec 30, 2016 at 2:54 PM, The Cromicus Productions <
>>>> wrote:
>>> > Hi everyone,
>>> >
>>> > I would like to know if there is an easy way to remove the motion
>>> > of the center of mass of a molecule after I have obtained the
>>> > trajectory (.mdcrd and .mdvel) files.
>>> >
>>> > Thanks a lot,
>>> >
>>> > Sebastian
>>> > _______________________________________________
>>> > AMBER mailing list
>>> >
>>> >
>>> >
>>> _______________________________________________
>>> AMBER mailing list
> _______________________________________________
> AMBER mailing list

Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
AMBER mailing list
Received on Tue Jan 03 2017 - 06:30:02 PST
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