Hi
I am confused. The inputs for two cpptraj versions are not identical.
Hai
> On Oct 25, 2016, at 1:01 AM, Saman Yousuf ali <saman.yousufali64.yahoo.com> wrote:
>
> Dear All,I have calculated RMSD around a residue ( 5A nearby) using two different version of cpptraj version 15 and 16 and got different results, reference and target mask during calculation was not same for both versions. The command I am using in cpptraj: Input(cpptraj version 15 bug fix)====================# Step 1. Force cpptraj to set active reference for topology.
> # Only load 1 trajectory frame.
> parm complex.prmtop
> reference ../../../complex.inpcrd [R0]
> trajin reimaged_complex.mdcrd 1 1
> # Blank action
> unstrip
> run
> clear trajin
> # Step 2. Now read in entire traj.
> trajin reimaged_complex.mdcrd
> # Create another reference, [R1]. This one will work with distance based masks.
> reference ../../../complex.inpcrd [R1]
> # Now execute rms command
> rmsd rms_test :536<:5.0&.CA,N,C ref [R1] out rms_test.dat
> strip :WAT
> strip :Na+
>
> Target mask: [:536<:5.0&.CA,N,C](69)Reference mask: [:536<:5.0&.CA,N,C](69)
> Input(cpptraj version 16)====================parm complex.prmtop
> trajin reimaged_complex.mdcrd
> rms first :536<:5.0&.CA,N,C out rms_test.dat
> strip :WAT
> strip :Na+
>
> Target mask: [:536<:5.0&.CA,N,C](32)
> Reference mask: [:536<:5.0&.CA,N,C](32)
> I do not know which one of the above is best for calculating active side rmsd.
>
> Anyone can explain this to me please?
>
> Best Regards, Saman Yousuf Ali
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Received on Mon Oct 24 2016 - 22:30:03 PDT
