Following the AmberTools15 manual (p. 552), I’m using the following input scrip to do a per-residue RMSD calculation:
parm complex_solv.prmtop
trajin prod_0-100ns.nc 1 10000 10
reference complex_solv.inpcrd [struct0]
rmsd A :11-125 ref [struct0] perres perresout PRMS.dat range 11-125 perrescenter perresmask &!.H,N,CA,HA,C,O
run
xmgrace PRMS.dat
Obviously there is something wrong with the script because instead of producing an x-axis with residue numbers, the x-axis represents frame number.
I’d appreciate any suggestions on how to improve the script to generate per-residue RMSD averaged over the trajectory time.
Regards
George
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Received on Tue Aug 18 2015 - 08:00:06 PDT
