Hi,
On Fri, May 15, 2020 at 2:51 AM DHEERAJ CHITARA <rs138.iiita.ac.in> wrote:
> trajin test.0050000_0050050.crd
> .......
> trajin test.0249950_0250000.crd
> strip :Na+, WAT, LIG
> center :5-305
> rms first mass :5-305
> atomicfluct out test_aq.rmsf_ca.dat .CA byres
> run
This will calculate the RMSF for CA atoms, after fitting to the first
frame. Note that the 'center' command is unnecessary since the
subsequent 'rms' command will move the system anyway. You may want to
autoimage prior to the 'rms' command if your system is not a monomer.
If you wanted to calculate to the average structure instead you would
first have to calculate the average structure (with the 'average'
command) and perform the 'rms' fit to that reference (via 'reference'
or 'ref <name>' keyword after loading the reference, see the manual
for full syntax).
> trajin test.0050000_0050050.crd
> .......
> trajin test.0249950_0250000.crd
> autoimage
> strip :Na+, WAT, LIG
> atomicfluct out test_aq.rmsf_ca.dat .CA byres
> run
This is probably not what you want. You dont do any fitting prior to
the atomicfluct command, so your rmsf will contain contributions from
global rotation/translation.
Hope this helps,
-Dan
>
> Which is the correct way to calculate RMSF with the first frame as
> reference and average frame as reference?
>
> Advance thanks for the suggestions.
>
> --
> ----
> Dheeraj Chitara
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Received on Mon May 18 2020 - 09:30:03 PDT
