AMBER: question about ptraj

From: Ioana Cozmuta <>
Date: Wed, 30 Jul 2003 15:07:21 -0700 (PDT)

Hi amber users,

I am trying to use the following ptraj script to do some diffusion, rdf

trajin MTS_nve_1Kz15.dcd 60 6860 100
diffusion :SPM :801-26516 0.2 average DiffSPMKz15
diffusion :K+ :799 0.2 average DiffKz15
radial RDF_Kz15_SPM 0.05 8.0 :SPM :799
radial RDF_NVEk_OO 0.05 8.0 :801-26516.O
radial RDF_MTS_HH 0.05 8.0 :801-26516.H
radial RDF_MTS_OH 0.05 8.0 :801-26516.* go

I do not understand why my job stops with the message
diffusion:solvent mask not specified

I do not understand how can I define the mask in the ptraj file. If I
want to use a range of residue numbers and not the residue name, if I want
to use for example a list of residue numbers that should be included in
the diff/rdf calculations, if I want to use some atoms only from a range
of residue names. I think the manual is not explicit enough on this.
If anyone can point me to a place where the definition of the mask is
explained I would appreciate that.
On the amber archive list it's suggested to use

radial rdf_DNA-wat 0.05 8.0 :WAT :1-16
diffusion :WAT average time 0.5
and I am trying to use this format.

Thank you,

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Received on Wed Jul 30 2003 - 23:53:01 PDT
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