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
Received on Tue Apr 14 2020 - 11:30:03 PDT
