Hi Fabricio,
I agree with Jason that you should probably try to use "igb1" and "igb2" in
the *.RST file. I was using Amber 11 and it worked for me. Here is my *.RST
file.
# r restraint for com of group1 and group2
&rst iat=-1,-1, r1=0., r2=5.5, r3=5.5, r4=20., rk2 = 1.,
rk3 = 1.,
igr1=2,3,4,6,8,9,11,13,15,
igr2=17,21,23,24,28,37,
&end
Best,
Mo
On Wed, Sep 19, 2012 at 1:26 AM, Fabrício Bracht <bracht.iq.ufrj.br> wrote:
> Hello.
> Before modifying my files, I decided to see if I could run the test
> simulations located at
> $AMBERHOME/test/cuda/nmropt/pme/jar_distance_COM/ . I ran the command
> " ./Run.jar_pbc " and the simulation failed. The error message in the
> mdout file was:
>
> CUDA (GPU): Implementation does not currently support the use of
> Jarzynski simulations.
> Require jar == 0 (default).
>
> Input errors occurred. Terminating execution.
>
> The example from $AMBERHOME/test/cuda/nmropt/pme/distance_COM/ also
> fails. The error message is:
>
> CUDA (GPU): Implementation does not currently support the use of COM
> simulations.
> Require iat(2) >= 0
>
> I have already updated amber12 and ./patch_amber.py says that there
> are no updates to apply. Am I doing something wrong?
>
> Thank you
> Fabricio
>
> 2012/9/18 Jason Swails <jason.swails.gmail.com>:
> > On Tue, Sep 18, 2012 at 10:25 PM, Fabrício Bracht <bracht.iq.ufrj.br>
> wrote:
> >
> >> Hello. Thank you for the reply. It really was kind of stupid to me to
> >> leave the double-quote open. As for the / character missing, there is
> >> no second line in my file. The email server must have formatted the
> >> text, and the result was a second line. But anyway, thank you for the
> >> tip.
> >> I have corrected the input and the dist.RST file now looks like this
> >>
> >> # Distance restraint for chain A and B (center of mass)
> >> &rst restraint="distance (com(1-33.N,CA,C),com(34-66.N,CA,C))", r1=0.,
> >> r2=11., r3=11., r4=35.0, rk2 = 30., rk3 = 30.,
> >>
> >> When I type the pmemd command, a warning appears on screen stating that:
> >>
> >> At line 990 of file nmr_calls.F90 (unit = 33, file = 'dist.RST')
> >> Fortran runtime error: Cannot match namelist object name restraint
> >>
> >> I have simply copied and modified a bit the lines on the amber12
> >> manual that state:
> >>
> >> The following are all examples of valid restraint definitions:
> >> restraint = "distance( (45) (49) )"
> >> = "angle (:21.C5’ :21.C4’ 108)"
> >> = "torsion[-1,-1,-1, com(67, 68, 69)]"
> >> = "angle( -1, plane(81, 85, 87, 90) )"
> >> = "angle(plane(com(9,10),:5.CA,31,32),plane(14,15,15,16))"
> >> = "coordinate(distance(:5.C3’,:6.O5’),-1.0,distance(134,-1),1.0)"
> >>
> >
> > This syntax is specific to sander. Look at page 202 of the Amber 12
> manual
> > where it describes the "restraint" variable in the &rst namelist. In
> that
> > description it says:
> >
> > New as of Amber 10 (sander only), users may now use a "natural language"
> > system to define restraints by using the RESTRAINT character variable.
> >
> > If you want to use pmemd.cuda and/or pmemd with NMR restraints, you will
> > need to use the "iat" variable (and "igr1" and "igr2" variables for COM
> > distances). In light of this, I actually never use the "natural
> language"
> > input myself.
> >
> > Note that pmemd supports only a relatively small subset of the Amber
> nmropt
> > functionality, and pmemd.cuda supports an even more limited set. As a
> > result, if you think you have an input file that should work for pmemd
> but
> > doesn't, try it on sander. If it works, then most likely you've hit a
> > pmemd limitation.
> >
> > HTH,
> > Jason
> >
> > P.S. As another note -- check out the $AMBERHOME/test/nmropt/ test cases
> > (only present after you've applied all Amber12 bug fixes). The Makefile
> > lists all of the tests that work with pmemd (and you can find the
> > pmemd.cuda-compatible ones in $AMBERHOME/test/cuda/nmropt). My
> suggestion
> > is to adapt one of these input files to your system (since these are
> known
> > to work for pmemd and pmemd.cuda, respectively).
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Sep 18 2012 - 23:00:03 PDT
