Dear Jitrayut,
You can do this with the ptraj program. You can do this simply by using
the following input file;
trajin trajectorycoordfilename e.g. mdcrd
strip :WAT (assuming your waters have the residue name WAT)
trajout outputtrajectoryfilenameofyourchoice e.g. mdcrd.dry
go
You can then invoke ptraj in the following way;
ptraj prmtop < ptrajinputscript > ptrajinformationoutputfilename
This is quite a simple way of doing it but hope it is of some help. It
is explained in the ptraj section of the manual as well.
simon
==========================================================
On Tue, 2006-06-13 at 02:50 +0700, jitrayut jitonnom wrote:
> Dear amber users
>
> I am a new users for amber so could anyone explain me about how to
> strip waters in a trajectorie file that obtained from explicit MD ? or
> maybe, what is an example of the script to do this ? These are my
> questions needed the answers from anyone.
>
> Thanks in advance for any suggestions
>
> Best regard
>
> Jitrayut
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Jun 14 2006 - 06:07:14 PDT
