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
>
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Received on Tue Apr 14 2020 - 12:00:02 PDT
