Hi all,
I ran a 1µs simulation of a short peptide interacting with a 206aa protein.
The protein has a stable "core" (residues 5-85 and 118-204) and some
flexible regions (1-4, 86-117, and 205-206). What I would like to do is use
cpptraj to go through my trajectory aligning the core of the protein, and
print a pdb file every 1ns, so that my output would be 1000 pdb files with
the core of the protein in the same position. I plan to then use these 1000
pdb files to map the average position of the peptide around the core of the
protein in another program. I have previously aligned the core of this
protein to a reference .rst file to do RMSD calculations using this command:
parm A_solvated.prmtop
trajin A_centered.mdcrd
reference A.rst
rms ToMember1 :5-85,118-204&!.H= reference out A_RMSDtoRef.out
So I'm guessing the alignment procedure would look similar? Also my
trajectory was written in 10ps steps, so I'd like to basically print every
100th step as a pdb file after alignment. Any advice would be helpful.
-Chris
--
Christopher Warren
PhD Candidate
Lab of David Shechter
Department of Biochemistry
Albert Einstein College of Medicine
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Received on Thu Apr 19 2018 - 10:30:02 PDT
