AMBER: Ptraj and order of operations

From: Furse, Kristina Elisabet <>
Date: Mon, 11 Jul 2005 19:26:09 -0500


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

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

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

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...

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Received on Tue Jul 12 2005 - 01:53:00 PDT
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