Hello all,
I am trying to get a single point energy and force calculation in the
format listed earlier.
This input file
> Single Point energy and Force calculation
> &cntrl
> &debugf
> do_debugf = 1, imin = 0,
> dumpfrc = 1,
> /
>
> gives the error:
error in reading namelist cntrl
>
Unfortunately this error only appears once on
http://code.google.com/p/pbsa/source/browse/trunk/BSD/debug.f?spec=svn105&r=105and
does not appear in the AMBER11 manual.
How can I re-write the input file to get rid of this error? I apologize
ahead of time if this is an obvious error. I've checked the obvious
sources and can't find further information.
thanks in advance!
-Dave
I googled this and found it only once in the
On Fri, Mar 2, 2012 at 9:47 AM, Brian Radak <radak004.umn.edu> wrote:
> Hi Dave,
>
> There may be a more elegant way to get the forces, but try checking the
> AMBER manual under "Sander basics - Getting debugging information." The
> appropriate flags will print a file called "forcedump.dat" that will
> contain the desired information (although in standard AMBER units). For a
> large system, it might be a little difficult to discern the format, so try
> a small system first.
>
> Regards,
> Brian
>
> On Fri, Mar 2, 2012 at 9:25 AM, David Condon <dec986.gmail.com> wrote:
>
> > Hello AMBER community,
> >
> > I wish to do a very simple force calculation on small molecule with
> AMBER.
> >
> > I want to print out the results in the following manner:
> >
> > Center Atomic Forces (Hartrees/Bohr)
> > > Number Number X Y Z
> > > -------------------------------------------------------------------
> > > 1 1 -0.013840472 0.006184192 -0.017449443
> > > 2 8 -0.001254021 0.002478109 0.015430637
> > > 3 6 0.012193124 -0.002253820 -0.001928590
> > > 4 1 0.000604761 -0.007533336 -0.004640358
> > > 5 1 0.003751142 0.000636577 -0.007111325
> > > 6 6 0.004728352 0.004732434 0.025251443
> > > 7 1 0.000904130 0.006715029 0.003339335
> > > 8 8 0.007736524 -0.011316799 -0.011050874
> > > 9 6 -0.004283540 -0.015736246 0.008412823
> > > 10 1 0.003474074 -0.001951822 -0.008669195
> > > 11 7 0.012319615 0.027536212 -0.005742801
> > > 12 6 -0.003189597 -0.007040811 0.001403318
> > > 13 1 -0.002240575 0.002373720 0.008319431
> > > 14 6 0.008355495 0.006783900 -0.003055669
> > > 15 1 0.001598312 -0.000591626 -0.001304996
> > > 16 6 -0.015077408 0.028104077 0.027507462
> > > 17 7 0.009398325 -0.028375870 -0.033423192
> > > 18 1 -0.003575222 -0.006089736 -0.003293851
> > > 19 1 0.000373009 -0.006591262 -0.004007055
> > > 20 7 0.012406423 0.004165366 -0.005989237
> > > 21 6 -0.020034781 -0.032436161 0.007580551
> > > 22 8 0.021997410 -0.018905942 -0.001355500
> > > 23 6 -0.010291212 0.024399684 0.002101796
> > > 24 1 -0.004747313 -0.004373461 0.001623225
> > > 25 6 -0.024300537 0.001167487 -0.008324266
> > > 26 1 -0.001727523 0.017539246 0.005831803
> > > 27 8 -0.001892817 0.025892146 0.016631928
> > > 28 8 0.004809960 -0.010051110 -0.004173842
> > > 29 1 0.001235967 -0.005074795 0.004080807
> > > 30 1 0.000568397 -0.000385381 -0.005994365
> > >
> >
> > How can I get AMBER to print out results like this? By that I mean, how
> > can I write the input file so the results will be printed in the same
> > manner?
> >
> > Thanks for your time!
> > -Dave
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> ================================ Current Address =======================
> Brian Radak : BioMaPS
> Institute for Quantitative Biology
> PhD candidate - York Research Group : Rutgers, The State
> University of New Jersey
> University of Minnesota - Twin Cities : Center for Integrative
> Proteomics Room 308
> Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> Department of Chemistry : Piscataway, NJ
> 08854-8066
> radak004.umn.edu :
> radakb.biomaps.rutgers.edu
> ====================================================================
> Sorry for the multiple e-mail addresses, just use the institute appropriate
> address.
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Received on Fri Mar 16 2012 - 13:30:02 PDT
