Re: [AMBER] Deleting multiple atoms in xleap

From: Jason Swails <>
Date: Sat, 18 Jul 2015 07:29:36 -0700

On Fri, Jul 17, 2015 at 5:32 AM, jacob wick <> wrote:

> Hi everyone,
> I am dealing with some modified residues and using some already know
> procedures I have constructed structure of my system with correct partial
> charges. Now, when I am loading it in xleap, I can see many non bonded
> atoms hanging around my structure (Pl. see the attached image). These atoms
> are of no use for me and I would like to delete them.
> The problem is the number of these dots are over 400 and deleting it
> manually in xleap is very difficult. So, is there is any way by which I can
> removes such atoms at a time or with less human effort.

‚ÄčThose atoms must be present or defined in some kind of input file. Either
the PDB, mol2, prep, or Amber library file. You should delete the unwanted
atoms from the source file rather than deleting them inside xleap or tleap.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Sat Jul 18 2015 - 07:30:02 PDT
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