[AMBER] cpptraj: rms around 5 angstrom of ligand issue.

From: Saman Yousuf ali <saman.yousufali64.yahoo.com>
Date: Tue, 25 Oct 2016 05:01:07 +0000 (UTC)

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
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 - 22:30:02 PDT
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