VMD-L Mailing List
From: Ashar Malik (asharjm_at_gmail.com)
Date: Mon Jun 12 2017 - 06:04:53 CDT
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start vmd
load 1bna into vmd
use the following commands
set only_Phosphates [atomselect top "name P"]
$only_Phosphates writepdb phosphate_only.pdb
this will make a new pdb file called phosphate_only,pdb and inside it you
will only have phosphate atoms.
This command
*set only_Phosphates [atomselect top "name P"]*
will select all phosphates which have atom names "*P*" which is usually the
case with DNA molecules.
Hope this helps.
-- Best, /A On Mon, Jun 12, 2017 at 10:07 PM, jrhau lung <jrhaulung_at_gmail.com> wrote: > Dear Roshan: > You can use UCSF chimera, fetch the structure by input ID (1bna). All > phosphate can be selected by select -> chemistry -> functional group -> > phosphate > And save the coordinate of selected phoaphate by file -> save PDB -> use > the save select atom only. It will save what you want. Hope this help. > > sincerely, Jrhau > > > 2017-06-12 17:19 GMT+08:00 Roshan Shrestha <roshanpra_at_gmail.com>: > >> I want to extract coordinates for Phosphate from the pdb file, to be >> specific from 1bna.pdb inorder to create the pdb file of phosphate for its >> simulation. Is there any way to do it ? Thanks >> >> -- >> Roshan Shrestha >> Graduate Student >> Central Department of Physics,Tribhuvan University >> Kathmandu,Nepal >> >> >> > -- Best, /A
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