VMD-L Mailing List

From: Joshua Adelman (jla65_at_pitt.edu)
Date: Sat Dec 18 2010 - 09:07:59 CST

Hi Siddesh,

Was it really reasonable to think that I knew what the exact dimensions of your system to give you the correct ranges in the atomselect? It was meant as a suggestion of form.

I would suggest taking a look at the VMD manual, specifically:
http://www.ks.uiuc.edu/Research/vmd/current/ug/node133.html

You might consider using the minmax command and the appropriate atomselections to determine the ranges you want.

Josh

On Dec 18, 2010, at 9:14 AM, siddesh southekal wrote:

> Thanks for the reply.
> yes,Josh is right , moreover this selection can be used to select unwanted ions apart from water molecules.However,
> set sel [atomselect top "{y > -20 and y < 20}] just selects atoms on one side of membrane
> Is there a way to get the length of the y axis ,
> (or the maximum length of y-axis ? ) so that i can make the selection for a particular range ?
> thanks,
> Siddesh
>
> On Fri, Dec 17, 2010 at 5:31 PM, Joshua Adelman <jla65_at_pitt.edu> wrote:
> You don't want to use the 'within' keyword, since that will carve out a strangely shaped box (it's drawing a sphere around each protein atom and only selecting atoms within the sphere). You want something more like:
> set sel [atomselect top "{y > -20 and y < 20}]
>
> That will give you a slice of the system that removes extra water above and below your membrane slab.
>
> The other thing you'll have to watch out for is that atomselect will truncate water molecules that straddle the interface of the slab, resulting in a set of atoms that include incomplete water molecules. So you then need to then go back through and get the complete set of atoms using something like:
> set B [lsort -unique [$sel get resid]]
>
> and then using that list to get the set of atoms that you want.
>
> Best of luck.
>
> Josh
>
>
>
> On Dec 17, 2010, at 9:29 AM, Ajasja Ljubetič wrote:
>
>> I think you have to say
>> set selwater [atomselect top "name OH2 and within 10 of protein "]
>>
>> (*delete the not*)
>>
>> It's always best to view selections graphically.
>> You can put the selection string under representations -> selected atoms and see what you have selected. I usually set the drawing method to CPK.
>>
>> Regards,
>> Ajasja
>>
>> On Fri, Dec 17, 2010 at 14:18, siddesh southekal <siddeshonline_at_gmail.com> wrote:
>> Dear all,
>>
>> I have a pdb file (after 20 ns MD run ) with a membrane protein (GPCR) embeded in the lipid bilayer with buffer around .There is excess of water molecules in this file . I want to remove this excess buffer such that i have water molecules only 10 A above and below the protein .(say around 15 A around the lipid ) .The membrane normal is in y direction.
>> I would be using the truncated file for MD simulation using AMBER.
>> I tried -
>> set selwater [atomselect top "name OH2 and not within 10 of protein "]
>> But whn i try to save the selection the pdb file is blank.How do i exactly do this?
>> I would appreciate any suggestions
>> Thanks ,
>> Siddesh
>> Universitaet Bonn
>>
>
>
>