[AMBER] strip waters using distance criteria

From: Thomas Evangelidis <tevang3.gmail.com>
Date: Fri, 23 Sep 2016 15:23:07 +0200

Greetings,

I want to strip the waters that are further than 4 Ang. from the ligand. I
tried to do it with cpptraj like this:

​cpptraj complex.prmtop << EOF
reference complex.prod_GB.nc lastframe
trajin complex.prod_GB.nc 11 15
mask "(:LIG >:4.0) & :WAT" maskout delWAT4Ang_mask.txt
strip "(:LIG >:4.0) & :WAT" outprefix complex2
trajout complex.MMGBSA_GB.WAT4Ang.nc
go
quit
EOF

But cpptraj strips all the waters and leaves only the ligand and the
protein. What am I doing wrong?

thanks,
Thomas​

-- 
======================================================================
Thomas Evangelidis
Research Specialist
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/1S081,
62500 Brno, Czech Republic
email: tevang.pharm.uoa.gr
          tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

Received on Fri Sep 23 2016 - 06:30:03 PDT