Your trajout command says to process frames 1 to 200. If you want 1 pdb
file, specify 1 frame.
On Jul 18, 2011 11:01 AM, "George Tzotzos" <gtzotzos.me.com> wrote:
> Hi everybody,
>
> The sequence of actions below is self explanatory:
>
> 1. strip all but closest water molecules to a given protein residue (:124)
and generate a pdb file (new.pdb)
>
> 2. process a 2ns trajectory file by keeping only the closest water
molecules and generate a new trajectory file (new.mdcrd)
>
> 3. create new topology files from new.pdb using tleap
>
> The above scheme works with the following hiccup.
>
> In step 1., the script
>
> trajin prod_2ns.mdcrd
> center :1-124 mass origin
> image origin center familiar
> solvent byres :WAT
> closest 4 :124.N first no image
> strip :Na+
> trajout test.pdb pdb 1 200 1
>
> produces 200 individual pdb files.
>
> My questions:
>
> Is there a way to produce only one new.pdb file? Furthermore, if the
working directory contains other trajectories (e.g. prod_4ns, prod_6ns,
etc.), the script scans them all - although they are not specified in the
first line of the script. Any suggestions why so?
>
> Is there a way to merge the script of step 1 with that of step 2, below?
>
> trajin prod_2ns.mdcrd
> trajout prod_closest_WAT_2.mdcrd netcdf
> center :1-142 mass origin
> image origin center familiar
> solvent byres :WAT
> closest 4 :124.N first no image
> strip :Na+
>
>
>
>
>
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Received on Mon Jul 18 2011 - 09:30:03 PDT
