Re: removing water from DCD

From: Alessandro Pedretti (alessandro.pedretti_at_unimi.it)
Date: Thu Jul 21 2005 - 01:55:34 CDT

Dear Julie,
try to use VEGA ZZ, available for free at http://www.ddl.unimi.it/vega
1) Open your MD (File -> Open). If the DCD file doesn't have the same file
name of the PDB, you must open the PDB file (File -> Open) and thus the DCD
file (Calculate -> Analysis, click the "open" button).
2) Unselect the waters (View -> Select -> No waters)
3) Save the trajectory file (File -> Save trajectory), choosing your
preferred file format (e.g. DCD) and checking "Active only" in the Options
box.

To reopen the DCD file without waters, you need a compatible PDB file:

4) Remove the invisible atoms (Edit -> Remove -> Invisible atoms)
5) Save the PDB file (File -> Save As...)

In this way, you can obtain a PDB file without waters.

Best regards

        Alessandro Pedretti

----- Original Message -----
From: "Stern, Julie" <jvstern_at_bnl.gov>
To: <namd-l_at_ks.uiuc.edu>
Sent: Thursday, July 21, 2005 2:49 AM
Subject: namd-l: removing water from DCD

> Hello,
> What is the best way to remove water
> from the DCD file after it has been created?
> Are there any postprocessing tools for this?
>
> Thanks.
>
> --Julie
>
>

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