Hi,
What version of cpptraj are you using? When cpptraj exits, are you
sure there are no error messages? What is its error status (i.e. 'echo
$?')?
-Dan
On Wed, Jan 27, 2016 at 2:24 AM, richa anand <richaaanand.gmail.com> wrote:
> 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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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Jan 27 2016 - 07:00:04 PST
