VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Thu Feb 12 2015 - 20:56:57 CST

i am not an expert - but your problem "might" be because of these 2 reasons
-

1) the residue you are looking for DOESN'T exist in the frame that you are
trying to find it in.

2) you have NOT loaded the trajectory/data.

I am not sure about the second might be MORE closer to your error.

On Fri, Feb 13, 2015 at 3:32 PM, Monika Madhavi <monikamadhavi_at_gmail.com>
wrote:

> Dear Ashar,
> Thats not a problem in my case. I have only water in my dcd file. No
> proteins.
>
> Monika
>
> Monika Madhavi
> Department of Physics
> University of Colombo
> On Feb 13, 2015 7:51 AM, "Ashar Malik" <asharjm_at_gmail.com> wrote:
>
>> When solvation is done, water molecules overlapping protein are deleted.
>> So there are chances that if you choose a random number it may not have a
>> water molecule against it. Also does your trajectory hold only water
>> molecules, otherwise you have to resolve the atomselect command to add
>> specific keywords indicating that the residue is suppose to be water and
>> NOT protein.
>> On Feb 13, 2015 2:54 PM, "Monika Madhavi" <monikamadhavi_at_gmail.com>
>> wrote:
>>
>>> Thank you everyone. When "" used, atomselect worked. However now I am
>>> getting a different error. My task is to randomly select a water molecule
>>> from a dcd file and write their coordinates to a new pdb file. I used the
>>> following script.
>>>
>>> set random [expr round(rand()*100)]
>>> set sel [atomselect top "resid $random"]
>>> $sel writepdb out.pdb
>>> $sel delete
>>>
>>> I am getting an error saying; atomsel: frame -1 out of range for
>>> molecule 1
>>>
>>> Can you please suggest a solution?
>>>
>>> Thanks
>>> Monika
>>>
>>> On Thu, Feb 12, 2015 at 2:53 PM, Tristan Croll <tristan.croll_at_qut.edu.au
>>> > wrote:
>>>
>>>> That will select every resid 5 from all the segments in your structure.
>>>> The keyword you're looking for is "residue" (or, if you like, "segname XXX
>>>> and resid 5").
>>>>
>>>>
>>>>
>>>> Tristan Croll
>>>> Lecturer
>>>> Faculty of Health
>>>> School of Biomedical Sciences
>>>> Institute of Health and Biomedical Engineering
>>>> Queensland University of Technology
>>>> 60 Musk Ave
>>>> Kelvin Grove QLD 4059 Australia
>>>> +61 7 3138 6443
>>>>
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>>>>
>>>>
>>>> > On 12 Feb 2015, at 5:44 pm, Monika Madhavi <monikamadhavi_at_gmail.com>
>>>> wrote:
>>>> >
>>>> > Dear all,
>>>> >
>>>> > I need to select all the atoms of a particular water molecule from a
>>>> dcd file and write it's coordinates to a separate pdb/dcd file. Can I do
>>>> this using atomselect in vmd tcl? I tried the following command but it
>>>> doesn't work.
>>>> >
>>>> > set sel [atomselect top {resid 5}]
>>>> >
>>>> > Thank you.
>>>> > Monika
>>>> >
>>>> > --
>>>> > W.A.Monika Madhavi
>>>> > Lecturer (Probation),
>>>> > Department of Physics,
>>>> > University of Colombo.
>>>>
>>>
>>>
>>>
>>> --
>>> W.A.Monika Madhavi
>>> Lecturer (Probation),
>>> Department of Physics,
>>> University of Colombo.
>>>
>> 

-- 
Best,
/A