VMD-L Mailing List

From: Kim, Kwiseon (kwiseon_kim_at_nrel.gov)
Date: Sun Feb 15 2004 - 09:09:07 CST

vmd-l: removing residues/fragments from the system
Try this.
---------
 
 readpsf  your.psf
 coordpdb your.pdb
 set sel [atomselect top "water and not within 5 of protein"]
 set deletelist [$sel get {segname resid}]
 set previtem {null 0}
 foreach item $deletelist {
   if {$item == $previtem} continue
   set previtem $item
   delatom [lindex $item 0] [lindex $item 1]
 }

 writepsf  yournew.psf
 writepdb yournew.pdb
---------
 
Kwiseon
 
-----Original Message-----
From: Satyavani Vemparala [mailto:vani@VITAE.CMM.UPENN.EDU]
Sent: Sat 2/14/2004 8:00 PM
To: vmd-l@ks.uiuc.edu
Cc:
Subject: vmd-l: removing residues/fragments from the system


Hello:

is there a way/ a script to remove certain fragments like water molecules
from both the PDB and PSF files? or even remove waters based on distance
from lipids/proteins?

after solvation of lipid bilayers , i need to remove certain water
molecules, and doing it in PDB files is simple, but then there is no
consistency between PDB & PSF files.

Thanks
Vani

--