On Tue, Nov 22, 2011, Charles Johnson wrote:
>
> I am currently trying to make a hydrogen bond RST file for a 9-mer RNA
> duplex. When I try and run makeDIST_RST i obtain the following error:
>
> # makeDIST_RST
> Currently configured for up to 5000 atoms
> Using MAP file /share/apps/amber11/dat/map.DG-AMBER
> ERROR no map function for H1 RG5 :data= 1 GUA H1 18 CYT N3 1.84 2.04
Starting with Amber11, the map.DG-AMBER file uses PDB version 3 residue
names. Hence, you need to build the RNA with a forcefield like ff10,
and use "G" and "C" instead of "GUA" and "CYT".
[You could also edit (a copy of) the map.DG-AMBER file to go back to the older
residue names, but I suspect your long-run needs would be better met by
updating to the current PDB/IUPAC standards. Either way, becoming familiar
with the contents of this file should pay dividends.]
...good luck...dac
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Received on Tue Nov 22 2011 - 11:30:04 PST
