From: Parker de Waal (
Date: Tue Sep 23 2014 - 21:49:32 CDT

Hi John,

Thanks for the tip. Unfortunately after looking for about 30 minutes or so
minutes Išve been unable to find any previous mailings or any guides
online regarding similar tasks.

If you could point me in a more specific direction I would greatly
appreciate it.


On 9/23/14, 10:00 PM, "John Stone" <> wrote:

>You can use VMD atom selections based on the atom coordinates along
>with "same residue as" to achieve what you're looking for. There are
>many examples in the user's guide and past mailing list discussions that
>will likely prove useful.
> John Stone
>On Wed, Sep 24, 2014 at 01:27:08AM +0000, Parker de Waal wrote:
>> Hello everyone,
>> I?ve recently been working with membrane protein simulations, generated
>>by the CHARMM-GUI membrane builder and simulated in AMBER, and am trying
>>to figure out a way to trim down on excess system padding (resulting
>>from the unoptimized GUI).
>> What I would like to do is be able to take the generated
>>protein/membrane PDB, select a rectangular region with origin x,y,z and
>>dimensions a,b,c, and then delete everything else that doesn?t fall
>>within that selection. This way I can reduce my atom count and help get
>>more ns/day for the simulation.
>> Does anyone know if this is possible in VMD, or perhaps another tool?
>> Best,
>> Parker
>NIH Center for Macromolecular Modeling and Bioinformatics
>Beckman Institute for Advanced Science and Technology
>University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>Phone: 217-244-3349