What version of cpptraj are you using? You might need a more up to
date version of cpptraj to use an on-the-fly reference from 'average'
for 'rms'.
-Dan
On Tue, Apr 14, 2020 at 2:41 PM Rana Rehan Khalid <ray.binm.gmail.com> wrote:
>
> Hi
> Thank you for your response, I thought
>
> rms ref MyAverage :1-194&!.H= (This line was for reference)
> The above script run fine on gpu
>
> But fail to run job on cpu cluster.
>
> Should I do this
>
> parm wet.complex.prmtop
> *reference min.rst*
> trajin md.mdcrd
> trajin md1.mdcrd
> rms first :1-194&!.H=
> average crdset MyAverage
> run
> rms ref MyAverage :1-194&!.H=
> matrix covar name l-covar :1-194&!.H=
> diagmatrix l-covar name l-modes out l-evecs.dat vecs 3 \
> nmwiz nmwizvecs 3 nmwizfile l.nmd nmwizmask :1-194&!.H=
> run
> rms ref MyAverage :1-194&!.H=
> projection LIGAND-DIMER evecs l-modes beg 1 end 3 :1-194&!.H=
> run
>
> Thanks
>
> Rehan
>
> On Tue, Apr 14, 2020 at 11:20 PM Elvis Martis <elvis_bcp.elvismartis.in>
> wrote:
>
> > Hi
> > You forgot to mention the reference file.
> > You must load a reference file using the “reference” key word after you
> > load your prmtop file
> >
> > On Tuesday, April 14, 2020, Rana Rehan Khalid <ray.binm.gmail.com> wrote:
> >
> > > Dear Amber User
> > >
> > > I am facing this error. Please help me in resolving this issue.
> > >
> > >
> > > Error: Could not get reference with name MyAverage
> > > Error: Could not initialize action [rms]
> > > 1 errors encountered reading input.
> > > ////////////////////////////////////////////////////////////
> > > /////////////////////////////
> > >
> > > parm wet.complex.prmtop
> > > trajin md.mdcrd
> > > trajin md1.mdcrd
> > > rms first :1-194&!.H=
> > > average crdset MyAverage
> > > run
> > > rms ref MyAverage :1-194&!.H=
> > > matrix covar name l-covar :1-194&!.H=
> > > diagmatrix l-covar name l-modes out l-evecs.dat vecs 3 \
> > > nmwiz nmwizvecs 3 nmwizfile l.nmd nmwizmask :1-194&!.H=
> > > run
> > > rms ref MyAverage :1-194&!.H=
> > > projection LIGAND-DIMER evecs l-modes beg 1 end 3 :1-194&!.H=
> > > run
> > > hist LIGAND-DIMER:1 bins 300 out lig-hist.agr norm name lig-1
> > > hist LIGAND-DIMER:2 bins 300 out lig-hist.agr norm name lig-2
> > > hist LIGAND-DIMER:3 bins 300 out lig-hist.agr norm name lig-3
> > > run
> > > ##############
> > > clear all
> > > readdata l-evecs.dat name Evecs
> > > parm wet.complex.prmtop
> > > parmstrip !(:1-194&!.H=)
> > > parmwrite out lig-modes.prmtop
> > > runanalysis modes name Evecs trajout lig-final.nc \
> > > pcmin -300 pcmax 300 tmode 1 trajoutmask :1-194&!.H= trajoutfmt netcd
> > >
> > > ////////////////////////////////////////////////////////////
> > > ////////////////////////////////////////////////////////////
> > >
> > > Regards
> > > Rehan
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> > --
> > Best Regards
> > Elvis Martis
> > Mumbai.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
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Received on Wed Jun 24 2020 - 09:30:05 PDT
