On Mon, Oct 26, 2009, Yunjie Zhao wrote:
> I want constrain a distance in my RNA system, but when I ran the input
> file, there are some errors.
>
> makeDIST_RST -ual 8col.wc -pdb rna.pdb -rst RST.wc
>
> here is my 8col.wc file:
> 1 GUA O6 12 URA H3 2.09 2.29
> * ***** ** ** ****** ** ***** *****
> * ***** ** ** ****** ** ***** *****
> * ***** ** ** ****** ** ***** *****
> * ***** ** ** ****** ** ***** *****
>
> and here is errors in my out put file:
> # makeDIST_RST
> Currently configured for up to 5000 atoms
> Using MAP file /export/home/zyj/amber9/dat/map.DG-AMBER
> ERROR no map function for H3 URA :data= 1 GUA O6 12 URA H3
> 2.09 2.29
The map.DG-AMBER file uses the (now-old) Amber residue names for
ribonucleotides, e.g. RU5, RU and RU3 for uracil, etc. Furthermore, it thinks
"GUA" is deoxy-guanidine (although that probably won't be a problem, unless
you have restraints to the 2' OH proton.
The simplest thing to do is to edit (a copy of) your map.DG-AMBER file, and
change the residue names to those in your prmtop file (change atom names if
needed as well.).
I'll put together an updated version of the map files, either as a bugfix, or
as part of the next AmberTools release.
Thanks for the report....dac
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Received on Mon Oct 26 2009 - 14:30:02 PDT
