Re: [AMBER] makeDIST command disfuntion

From: David A Case <>
Date: Mon, 13 Jan 2014 21:16:24 -0500

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).

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".

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.)

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.


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Received on Mon Jan 13 2014 - 18:30:02 PST
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