Hi Richa
Have you tried to input your .rst file as a reference. I see that you are
using .crd files as reference.
Try to use the following input (rmsd_cpptraj.trajin) file (modify it as per
your files specification).
trajin *.mdcrd
reference *.rst
autoimage
rms reference mass out RMSD.rms :1-258 .P,O3',O5',C3',C4',C5' , with fitting
I hope you are using below command
cpptraj -p *..prmtop -i rmsd_cpptraj.trajin > cpptraj.log
for reference you can also give the coordinates of the average structure
that you can calculate using your two *.crd files.
trajin your*.crd1 (mdcrd files)
trajin your*.crd2
strip :WAT,Na+
center :1-258 mass origin
image origin center familiar
average reference_avg.pdb pdb nowrap
I hope that helps
Vasantha
2016-01-27 10:24 GMT+01:00 richa anand <richaaanand.gmail.com>:
> Hi Amber users,
>
> I want to calculate RMSD value with reference to Average structure. For
> this I am using the following input file.
>
> trajin 1SI2_C.050480_050490.crd
> trajin 1SI2_C.050490_050500.crd
>
>
> autoimage
>
> strip :Na+,WAT
>
> reference AVERAGE_500_50000_C.crd [500_50000_crd]
>
> rmsd BB :1-258 .P,O3',O5',C3',C4',C5'ref [500_50000_crd] out
> avg.1SI2_C.001000_051000_siRNA_Backbone.rmsfit
>
> rmsd BB :1-258 .N,CA,C ref [500_50000_crd] out
> avg.1SI2_C.001000_051000_protein_Backbone.rmsfit
>
> rmsd BB :1-258 .P,O3',O5',C3',C4',C5',CA,C,N ref [500_50000_crd] out
> avg.1SI2_C.001000_051000_Complex_All.rmsfit
>
> rmsd BB :1-258 .CA ref [500_50000_crd] out
> avg.1SI2_C.001000_051000_Protein_Alpha.rmsfit
>
> run
>
> But I am not getting any result and cpptraj does not process co-ordinates
> after reading the frames. Result in output file is given below:
>
>
> [trajin 1SI2_C.050490_050500.crd]
> [1SI2_C.050490_050500.crd] contains 10 frames.
> [autoimage]
> AUTOIMAGE: To box center based on center of mass, anchor is first
> molecule.
> [strip :Na+,WAT]
> STRIP: Stripping atoms in mask [:Na+,WAT]
> [reference AVERAGE_500_50000_C.crd [500_50000_crd]]
>
>
> Can anybody suggest me what's wrong with my input file.
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Received on Wed Jan 27 2016 - 03:30:06 PST
