[AMBER] How to use makeDIST_RST without MAPping?

From: Jan-Philip Gehrcke <jgehrcke.googlemail.com>
Date: Mon, 23 Sep 2013 17:43:36 +0200


Short version:

It seems to be the default that a MAP/translation rule must be available
for every single atom listed in a 7/8-column makeDIST_RST input file. I
don't need this translation. Is there a way to *not* use atom name
mapping when running makeDIST_RST?

Longer version:

I am currently working myself into using sander for creating a
carbohydrate structural ensemble based on NOE distance restraints.

I want to use makeDIST_RST for translating quite a large number of
distance restraints to the DISANG format and use something like the
following command:

makeDIST_RST -ual distances -pdb system.pdb -rst rst.dist

All the resid-resname-atomname entries in my current '-ual' file are
unambiguous and have one corresponding match in the system.pdb file. In
other words, I currently do not need to make use of the MAP mechanism of

By default, makeDIST_RST seems to look for a translation rule for each
single atom listed in the '-ual' file. Since this is neither protein or
DNA in my case, the residue names I am using do not appear in the
default amber12/dat/map.DG-AMBER file. Since there are no translation
rules available, makeDIST_RST fails on the first line of my `distances`
file, with the error message:

ERROR no map function for H1 02u :data= 5 02u H1 4 47Y H5 2.87 3.79

I tried using something like

makeDIST_RST -ual distances -pdb system.pdb -rst rst.dist -map empty

but the error message persists. Without translation, makeDIST_RST seems
to refuse to fight.

Do I now really need to create a MAP file for my carbohydrate residues
that essentially implements a dummy translation?

 From my point of view, makeDIST_RST should allow for missing
translation rules as long as an atom is i) defined unambiguously and ii)
available in the PDB file. That way, also amber12/dat/map.DG-AMBER could
be much more sparse... most of the translations actually don't translate.

Do I oversee something? Thanks for valuable input,


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Received on Mon Sep 23 2013 - 11:30:03 PDT
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