AMBER Archive (2008)

Subject: AMBER: Combine mdcrd

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Fri Jan 04 2008 - 10:37:07 CST

I am getting weird structures by combining mdcrd with either one
combine_mdcrd.ptraj:

trajin prod1.mdcrd.gz
trajin prod2.mdcrd.gz
trajin prod3.mdcrd.gz
trajout prod1-3_no_wat_pop.mdcrd
strip :WAT
strip :POP

trajin prod1.mdcrd.gz
trajin prod2.mdcrd.gz
trajin prod3.mdcrd.gz
trajout prod1-3_no_wat.mdcrd
strip :WAT

Then:

ptraj my.prmtop < combine_mdcrd.ptraj

where my.prmtop is the one for the original trajectories to combine.

It deals of a protein complex in a POPC membrane, all in a water box. Even the
structure of the non-polymeric ligand is completely disordered. Of course, each
trajectory to combine is OK. If anything, prod1 was obtained with 0.002fs time
step, the other two with 0.0015fs timestep.

Should prmtop be regenerated (how?) to get all fitting? My final aim is to
carry out a cluster analysis.

Additionally, once the above is set in order, it is not clear to me how to add
to the ptraj script the request for rmsd for both the protein and the ligand.

Thanks
francesco pietra

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