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 - 09:30:04 PDT
