Re: [AMBER] DRMSD utility in cpptraj

From: Debarati DasGupta <>
Date: Tue, 21 May 2019 13:15:48 +0000

Hi Daniel,
Sorry that I appear totally confused and I guess it will make more sense if you scan the publications ( and (

I have a set of hotspots on my ABL kinase (ABL kinase with 70000 waters + 440 C3N molecules as cosolvent) which are characterized by specific cartesian coordinates. I do a simple distance command to calculate the distance across the frames on the closest C3N to my hotspot, These hotspots are in ligand space and not on the protein as such, then these publications talk of a DRMS versus time where the DRMS is the interatomic distance between their protein's active site residues and the DMSO probe (in their case)

If I have the location of the hotspot only by a x,y,z points I do not know how to go about doing a DRMS calculation over the trajectory?

Am i able to clearly say what the issue is>?

From: Daniel Roe <>
Sent: Monday, May 20, 2019 9:33 AM
To: AMBER Mailing List
Subject: Re: [AMBER] DRMSD utility in cpptraj


I'm not sure I understand what you're asking exactly. The distance
RMSD command uses all pairs of atoms in the specified mask, which
unless I'm mistaken is the same thing calculated by the equation you
posted. So e.g. if you do .1-3 the distance RMSD will be between:

atoms 1 and 2
atoms 1 and 3
atoms 2 and 3

Does that clear things up?


On Fri, May 17, 2019 at 4:45 PM Debarati DasGupta
<> wrote:
> Hi All,
> I want to calculate the DRMS (distance root mean square) between two MD snapshots a and b, DRMS [] , which is the intermolecular distances [] between pairs of non-hydrogen atoms my ligand (acetonitrile) and my active site location characterized by a x,y,z location. My system is ABL-Kinase with 440 acetonitrile molecules+7000 TIP3P waters. I see there is a DRMS utility in cpptraj in Page 650 of Amber18 manual but I am not able to understand how to feed in both the masks for DRMSD calculation across my entire trajectory.
> A sample input file I tried is
> parm ABL_complex.prmtop
> trajin A.mdcrd 1 1000 1
> trajin B.mdcrd 1 1000 1
> strip :WAT
> strip :Na+, Cl-
> drmsd :1-286 out C3N.out
> I get a file called C3N.out which prints out DRMS at each frame.
> But i did specify the i and j atoms for my distance calculation, then what DRMS value is being calculated when I give it just one mask that is residues :1-286?
> I am not able to make sense, any help will be appreciated.
> Thanks
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Received on Tue May 21 2019 - 06:30:03 PDT
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