[AMBER] DRMSD utility in cpptraj

From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Date: Fri, 17 May 2019 20:45:30 +0000

Hi All,

I want to calculate the DRMS (distance root mean square) between two MD snapshots a and b, DRMS [https://journals.plos.org/ploscompbiol/article/file?type=thumbnail&id=info:doi/10.1371/journal.pcbi.1002002.e006] , which is the intermolecular distances [https://journals.plos.org/ploscompbiol/article/file?type=thumbnail&id=info:doi/10.1371/journal.pcbi.1002002.e007] 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.

AMBER mailing list
Received on Fri May 17 2019 - 14:00:02 PDT
Custom Search