From: Monika Madhavi (monikamadhavi_at_gmail.com)
Date: Thu Feb 12 2015 - 20:32:40 CST

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
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>>> 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.
>>
>