Re: [AMBER] J-coupling restraints

From: Mickey Richards <mickey18385.gmail.com> Date: Thu, 21 Oct 2010 11:44:04 -0600

-- 
With best regards,
--Mickey Richards
Department of Chemistry
University of Alberta
email:  mickey18385.gmail.com
On Thu, Oct 21, 2010 at 10:45 AM, Mickey Richards <mickey18385.gmail.com>wrote:
> 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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