Hi Ilyas,
thanks! I had to adjust the permissions. The script works beautifully.
teşekkür ederim,
Dave
On Sat, Jul 30, 2011 at 11:39 PM, Ilyas Yildirim <
i-yildirim.northwestern.edu> wrote:
> 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 Sun Jul 31 2011 - 05:00:04 PDT
