Hello,
Based on the description in the manual, it seems like closest 10 :200 should
keep only the appropriate 10 water molecules. My comments are below:
On Fri, Aug 20, 2010 at 5:33 AM, Amor San Juan <amorsanjuan.yahoo.com>wrote:
>
> Is it possible to create a script in ptraj wherein both closest and strip
> commands are present?
>
> The script I used for closest:
>
> closest 10 :200
> image :WAT byres
> rms first mass :1-199
>
Did you specify a "trajout" anywhere? If you don't "trajout", then nothing
happens. It's helpful if you print out the entire script you used rather
than just the 3 lines you believe to be pertinent.
>
> The output trajectory (in order as it appears) contains :
> protein
> ligand
> waters(10) closest
> remaining tip3p water
>
> The script was able to find the ten closest waters near the ligand (:200)
> and write it in the output immediately afer the protein+ligand. The problem
> is the unselected waters (thousands and thousands) are still in the output.
> I tried to experiment on adding the strip command in above script but was
> not successful. Also, the other way around is from the output above I make a
> separate ptraj script to strip the waters 211-9199. Both are not successful.
>
How are they not successful? Do you get error messages? How did you try to
do this?
Good luck!
Jason
>
> My aim is to get an output trajectory (P+L+W10), such that
> P=protein,L=ligand,W10=ten closest waters. And feed this into MMPBSA for
> binding energy calculation.
>
> Amor
>
>
>
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Aug 20 2010 - 05:30:06 PDT
