Re: [AMBER] makeDIST command disfuntion

From: Jan Zalesak <>
Date: Tue, 14 Jan 2014 12:06:01 +0100

Thanks a lot David,

2014/1/14 David A Case <>

> On Mon, Jan 13, 2014, Jan Zalesak wrote:
> >
> > I am trying to run MD on RNA molecule with my NMR restraints.
> >
> > However when trying to convert my restraints using makeDIST_RST command
> > from 7-column file, I am still receiving this error:
> >
> > ERROR no map function for H1' URA :data= 1 URA H1' 2 CYT H6
> > 4.05 2.70
> >
> > I am working with AMBER9, could that be the problem?
> > If not, what are the current locations to set the path and variable for
> > this command?(there is AMBER12 installed but apparently do not work)
> You need to look at the map file you are using: it is probably in
> $AMBERHOME/dat/map.DG-AMBER, but that actually depends on what version of
> AmberTools you have (not on which version of Amber).
> Well I took a look at this one already but this doesn't seem to be where
the bug is.

> First, look at the output of "which makeDIST_RST", which should show you
> what the $AMBERHOME variable is. See if it is in a tree under "amber9" or
> under "amber12".

This one seem to be nailing the problem. So this one should give the
variable of $AMBERHOME?

cause it actually shows some nonsense like

> The reason I am asking all this: you say that "there is AMBER12
> installed"; one guess is that you are acutally running the programs (and
> using the mapfiles) from AmberTools12. In that case, what you see is
> expected, since URA is no longer a recognized residue (the PDB amd Amber
> moved to "U" sometime ago.)

I was hoping that this might be the actual solution (I tried all the
possible abbreviations yesterday, except U)... but neither U works
It is still giving the same error. This residue is indeed the first one in
the file. But even if I remove the first residue (URA) so the first is a
commonly recognized CYT, it gives the same error..

> If that doesn' help, is the restraint listed above the first one in the
> restraint file? That might help debug the problem: if earlier restraints
> are being processed correctly, try to see what is special about this one.
> ...dac
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Received on Tue Jan 14 2014 - 03:30:02 PST
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