VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Mon Jun 12 2017 - 06:04:53 CDT

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