Thank you so much Sir. Issue has been resolved.
Kind regards
On Wed, 24 Jun 2020, 9:14 pm Daniel Roe, <daniel.r.roe.gmail.com> wrote:
> 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
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> 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 Wed Jun 24 2020 - 09:30:06 PDT
