Sorry that was incorrect, I was replying on my phone and not being careful.
It's the trajin line that needs a frame specified if you only want 1 frame.
I don't think you can trajout only part of the input stream. Others may know
how to do that.
On Jul 18, 2011 11:17 AM, "George Tzotzos" <gtzotzos.me.com> wrote:
> Hi Carlos,
>
> Thanks for this. The problem (not a big one) is that the script produces
200 pdb files regardless of whether
>
> trajout test.pdb pdb 1 1 1
> trajout test.pdb pdb,
> or other permutation.
>
> Cheers
>
> George
>
>
>
> On Jul 18, 2011, at 6:06 PM, Carlos Simmerling wrote:
>
>> 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 - 09:30:06 PDT
