Kristina,
Simple answer is yes. With the exception of trajin and trajout each
action specificied is applied sequentially to the coordinates in the
order listed by the user in the input file (courtesy of the AMBER
manual).
On 7/11/05, Furse, Kristina Elisabet <kristina.e.furse.vanderbilt.edu> wrote:
> 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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Received on Wed Jul 13 2005 - 00:53:00 PDT
