AMBER Archive (2005)

Subject: AMBER: Ptraj and order of operations

From: Furse, Kristina Elisabet (kristina.e.furse_at_vanderbilt.edu)
Date: Mon Jul 11 2005 - 19:26:09 CDT

Hi-

Should the order of operations matter for the rms and image commands in ptraj?
For instance, in theory should the following two scripts output the same
coordinates?

trajin test.crd 2 2
reference test.pdb.1
trajout pass.pdb pdb
image center familiar
rms first out rmsCheckPass :554
go

trajin test.crd 2 2
reference test.pdb.1
trajout fail.pdb pdb
rms first out rmsCheckFail :554
image center familiar
go

I ask b/c I have run into a situation where the above scripts give pdb's which
have coordinates for solvent and counterions that are partly identical and
partly different--for instance, 8 out of 12 Na+'s have identical coordinates in
the two pdb's, while 4 have different coordinates. The system is a protein in a
periodic box. I can give more detail on the problem and system, and my labmate
Chris can talk code, but I thought I'd start with the simple question in case
there was a simple answer...

Thanks,
Kristina
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