VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Tue Jun 13 2017 - 08:27:08 CDT

You replied only to me - instead of the entire mailing list.

Anyway - you have to be more specific. When you say you want to extract
only one, which one?

Also I made a mistake.

The previous command with *[atomselect top "name P"]* selects only
phosphorous atoms and not phosphates. To fix this you have to use

*set only_Phosphates [atomselect top "name P or name OP1 or name OP2"]*
*$only_Phosphates writepdb phosphate_only.pdb*

Now the PDB should have all the phosphates (phosphorous atom and two
oxygens).

Going back to your question - you have to be specific in your criterion.

On Wed, Jun 14, 2017 at 1:14 AM, Roshan Shrestha <roshanpra_at_gmail.com>
 wrote:

> Thanks everyone. I did same as you guys told me. But, can we extract only
> single phosphate molecule instead of so many phosphate molecules from the
> pdb file.
>
> On 12 Jun 2017 4:49 pm, "Ashar Malik" <asharjm_at_gmail.com> wrote:
>
>> 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
>>
> 

-- 
Best,
/A
On Mon, Jun 12, 2017 at 11:04 PM, Ashar Malik <asharjm_at_gmail.com> wrote:
> 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
>
-- 
Best,
/A