David, thank you for your quick response. My replies are within the message
below:
On Thu, Oct 21, 2010 at 9:42 AM, David A. Case <case.biomaps.rutgers.edu>wrote:
> On Wed, Oct 20, 2010, Mickey Richards wrote:
> >
> > I would like to run a simulation using a J-torsion restraint for a single
> > dihedral angle. However, makeANG_RST does not seem to be compiled on my
> > system. The makeANG_RST.o file is also missing, which I gather is
> necessary
> > for this compilation.
>
> What happens when you cd to $AMBERHOME/src/nmr_aux/prepare_input and type
> "make install"?
>
The following error message appears:
" icc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -DBINTRAJ
-I../netcdf/include -o makeDIST_RST.o makeDIST_RST.c
Checkout succeeded: CCompL/22B033849A65
License file: /opt/intel/licenses/l_JCD8FM6B.lic
No server used
makeDIST_RST.c(62): warning #65: expected a ";"
} atma, atmb;
^
error: can't open file makeDIST_RST.o for write
compilation aborted for makeDIST_RST.c (code 1)
make: *** [makeDIST_RST.o] Error 1 "
>
> >
> > So, I would like to know if anyone has an example of a J-torsion
> restraint
> > after makeANG_RST has run, i.e. an example of the input that sander
> itself
> > uses?
>
> See tutorial A4, which has some examples of torsional restraints. There
> are
> also examples in Section 6.11.2 of the Users' Manual.
>
> ....dac
> I think I was unclear in my question. Both tutorial A4 and the Users'
Manual do have examples of torsional restraints, but these examples are on
the angle measurement itself - not for the J-coupling. If I want to
include the Karplus equation coefficients do I simply add a line including
the rjcoef1 -> rjcoef3 variables?
Thank you!
--
With best regards,
--Mickey Richards
Department of Chemistry
University of Alberta
email: mickey18385.gmail.com
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Received on Thu Oct 21 2010 - 10:00:04 PDT
