[AMBER] Trajectory processing using ptraj

From: James Starlight <jmsstarlight.gmail.com>
Date: Tue, 20 Jan 2015 18:53:41 +0100

Dear Amber users!

I'd be very thankful if someone provide me with small ptraj script which

1) fit input netCDF trajectory to amber the structure file.

2) chose subset of atoms from the trajectory- e.g I'd like to select only
protein residues from initial system consisted of solvent and ligand as well

3) Remove periodicity from new reduced system

3) save it in DCD

My steps are

# load full trajectory and fit the structure to it
trajin amd_go.nc 0 last 1
reference protein.inpcrd

# fitting to protein
center :1-361 mass origin
image origin center

# calculate RMSD for protein save new trajectoy w/o box
rms reference :1-361.CA out rmsd.dat
trajout md_proc.dcd dcd nobox

! in fact
1) it produce again full system trajectory without stripping the solvent
2) broken dcd file (is not recognized by VMD) but there is no problem if I
chose netCDF output again

Thanks for help,

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Received on Tue Jan 20 2015 - 10:00:05 PST
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