VMD-L Mailing List

From: Cun Zhang (apzc2529_at_gmail.com)
Date: Wed Aug 18 2010 - 03:25:21 CDT

I still don't know clearly what you want.
You mean specific water molecules, so you must think about how to select
these water molecules(math expresion may work, like "abs(x-5)<1 and water"
. I'm not sure)

When you select these molecules, you can use 'same residue as' to obtain
these residues and their ID.

I think you should read about Chapter 6 and Chapter 9 of vmd userguide. You
will get what you want.

On Wed, Aug 18, 2010 at 4:16 PM, deepti nayar <deeptinayar_at_gmail.com> wrote:

> Thanks for the reply
>
> But the problem here is that I want to find out residues that are
> interacting with specific water molecules (For which I can get their ID)
>
> Is it possible this way?
>
>
>
>
> On 18 August 2010 12:54, Cun Zhang <apzc2529_at_gmail.com> wrote:
>
>> Maybe you should write commands like the following
>>
>> [atomselect top "same residue as ( exwithin 5 of water )" frame 0]
>>
>> this command will select those atoms around water within 5 A, but not
>> including water in "frame 0".
>>
>> You can get more information from Chapter 6 and Chapter 9 of vmd
>> userguide.
>>
>>
>>
>> On Wed, Aug 18, 2010 at 2:14 PM, deepti nayar <deeptinayar_at_gmail.com>wrote:
>>
>>>
>>>
>>> Hi all
>>>
>>> I want to find out the residues that are interacting with water in a
>>> trajectory. Is there any script for this in vmd?
>>>
>>> -
>>>
>>
>>
>>
>> --
>> Blog: http://www.edwardpku.com/cun
>>
>
>
>
>
>
> 

-- 
Blog: http://www.edwardpku.com/cun