Hi,
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?
-Dan
On Fri, May 17, 2019 at 4:45 PM Debarati DasGupta
<debarati_dasgupta.hotmail.com> wrote:
>
> 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.
> Thanks
>
>
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Received on Mon May 20 2019 - 13:00:02 PDT
