AMBER Archive (2008)

Subject: AMBER: Combine mdcrd while stripping WAT problem

From: Francesco Pietra (
Date: Sun Jun 08 2008 - 10:40:07 CDT

With Amber10, on accumulating ns of trajectory, I am facing a problem
of trajectory analysis unresolved since Amber9 for the same protein
and environment, though for a different ligand.

The system is a large protein, carrying a large non-peptidic ligand.
It is embedded in a POP, TIP3P hydrated, membrane. Everything flows
correctly, 39% faster with pmemd with respect to sander.MPI.

What I am trying to do with ptraj is combining *.mdcrd while stripping WAT

While a complete action would be:

trajin prod1.mdcrd.gz
trajin prod2.mdcrd.gz
trajout prod1-#_no_wat.mdcrd nobox
strip :WAT
strip :POP

I tried simply:

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

That in view of using the *.prmtop for MD and in order not to change
the residue numbering.

With the same *.prmtop used for MD, the combined file does not load
cleanly with VMD. As expected.

I removed all WAT from *.prmtop. The same problem.

With Amber9 I had tried a larger number of combinations without
success. Now, the unedited *.mdcrd has become much too large to be
treated by VMD on my old Linux desktop with barely 1GB ram.

I can imagine to use (with the WAT stripped mdcrd) an antecedent
*.prmtop. Could you suggest from which stage? Or a better idea? Thanks

francesco pietra
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