Hi Brian,
thanks for pointing that out!
have a great weekend!
-Dave
On Fri, Mar 16, 2012 at 4:10 PM, Brian Radak <radak004.umn.edu> wrote:
> Simple mistake, the imin flag has to be in the cntrl section:
>
> Single Point energy and Force calculation
> &cntrl
> imin = 0
> &debugf
> do_debugf = 1, dumpfrc = 1
> /
>
> Regards,
> Brian
>
>
> On Fri, Mar 16, 2012 at 4:03 PM, David Condon <dec986.gmail.com> wrote:
>
> > 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.
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > 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.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 16 2012 - 14:00:03 PDT
