Dave - Check out the lines in makeCHIR_RST. You will see that makeCHIR_RST
creates a file called chiral_defs, which has all the chirality information
for aminoacids and deoxyribonucleotides. Put the chirality infos for RNA
nucleotides between "cat <<eof > chiral_defs .... eof". That should solve
the problem.
Ilyas Yildirim, Ph.D.
-----------------------------------------------------------
= Department of Chemistry - 2145 Sheridan Road =
= Northwestern University - Evanston, IL 60208 =
= Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
=
http://www.pas.rochester.edu/~yildirim/ =
-----------------------------------------------------------
On Sat, 30 Jul 2011, David Condon wrote:
> Hi all,
>
> I am attempting to run a simulated annealing protocol, but there are chiral
> inversions which prevent accurate measurement of dihedral angles. I figured
> chiral restraints would help. The file "gacc.z" was generated by ambpdb and
> should serve as the input, and "chi.z" should be the restraint output file,
> as described in page 196 of the AMBER9 manual. I copied the script
> makeCHIR_RST to the working directory, and added definitions for RNA.
>
> [con.malatya02 nmr]$ makeCHIR_RST gacc.z chi.z
> (using /bin/gawk)
> 0 chiral restraints generated in chi.z
>
> but as the above says, there is no output. I can find very little
> information on the net about this, unfortunately.
>
> Your help is much appreciated,
> -Dave
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>
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Received on Sat Jul 30 2011 - 21:00:03 PDT
