Dear Shahid,
with your rms command you perform an rms fit of your system onto your
metal atom and compute the resulting rmsd afterwards, which results in
0, of course: you can perfectly superimpose this atom in each of your
snapshots.
What you probably want to do is to perform an rms fit of your protein
(backbone) first, and then do a second rms calculation of the metal atom
without fitting. See the Amber manual of the rmsd command (subkeyword
"nofit") in the cpptraj chapter for details.
Best regards,
Anselm
Am 07.03.2019 um 12:21 schrieb shahid khan:
> Dear All,
>
> I have done the metalloprotein molecular dynamics using AMBER.
> I have to generate the RMSD for metal. My metal corresponds to residue
> number 250 and atom number 4100.
>
> I have checked the generation of RMSD by:-
>
> rms first out rmsd.xvg :250 time 0.01 (for residue)
> and
> rms first out rmsd.xvg .4100 time 0.01 (for atom number)
>
> But, I got the rmsd 0 throught the molecular simulation for both cases.
>
> I am not able to figure out how to resolve this issue.
>
> Thank you in advance
>
>
>
>
>
>
> Thanks & Regards,
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Received on Thu Mar 07 2019 - 04:30:02 PST
