Hi,
- a restart file (indicated by -r option to sander) contains only
one structure
- a trajectory file (indicated by a -x to sander) contains all the
structures that you want (maybe 50 in your case) depending on the value
of the ntwx keyword
Try giving to ptraj what you actually want. (there should be no problem)
Hope this helps,
Blas
---------------------------------------------------------------------------
Jose R. Blas
Molecular Modelling & Bioinformatics e-mail: jramon.mmb.pcb.ub.es
IRBB, Parc Cientific de Barcelona phone: + 34 93 403 71 55
C/Josep Samitier 1-5,
08028 Barcelona
On Wed, 26 Mar 2003, Venkata S Koppuravuri wrote:
> Hi
>
> I am trying to extract structures from the restart file that i have
> obtained after equilibration (using SANDER).
>
> The procedure that i have used ( i am not sure whether right or wrong)
>
> give the topology and restart files as inputs to ptraj and to output pdb
> files
>
> script used is ....
>
> --------
> ptraj topologyfile
> trajin restartfile
> trajout x.pdb pdb
> go
> -------
>
> The AMBER ptraj program gets executed and it says that it has only one
> frame to be visited, but actually i am supposed to have 50 in it. I am not
> sure whether the procedure that i have used is right or wrong
>
> can anyone please help me how to get all the structures.
>
> Regards
> -Venkat
>
>
>
Received on Thu Mar 27 2003 - 07:53:02 PST
