Re: [AMBER] Problem with stripping with a condition

From: Daniel Roe <>
Date: Thu, 20 Sep 2018 08:49:44 -0400


First, what version of cpptraj are you using?

Second, the way you have specified your mask, residues 1 to 100 will
always be removed (since by definition they are 0.0 Ang. from
themselves). If you don't want 1-100 removed, you have to put an "and
not" part of the mask, e.g.

strip (:1-100<:20.0)&!:1-100

Third, note that as stated in the manual distance-based masks in
general do *not* update each frame; they are instead based on the
"active" reference frame (default first reference frame loaded, can be
changed with 'activeref' command). The one command that does update
distance-based masks on a per-frame basis is the 'mask' command.

Hope this helps,

On Wed, Sep 19, 2018 at 11:57 AM Hadi Rahmaninejad
<> wrote:
> Hello Amber users,
> I am trying to remove atoms in a distance of some selected residues, so
> that according to ambmask I put this condition:
> trajin 03_equil.rst
> strip (:1-100<:20.0) outprefix cc.parm7
> trajout cc.traj
> However, when I do this stripping, it removes just my residues from 1 to
> 100 and not all the atoms within 20A from my selected residues. I tried
> different commands such as "strip :1-100<.20 " or "strip :1-100>:20.0" or
> even for waters inside that area: "strip (:1-100<:20.0)&:WAT" to see if
> the problem is my script. However, in all of them it just remove my
> selected residues. Have you ever had such a problem? I appreciate if you
> can help me about this,
> Thank you
> Hadi
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Received on Thu Sep 20 2018 - 06:00:02 PDT
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