Re: atom selection error

From: Peter Freddolino (petefred_at_umich.edu)
Date: Mon Dec 11 2017 - 14:26:26 CST

Did you do
BAS
or
name BAS

for the atom selection? I think my question suggests a likely solution...

On Mon, Dec 11, 2017 at 1:52 AM, Shahee Islam <shaheeislam726_at_gmail.com>
wrote:

> after loading psf followed by dcd in vmd rmsd trajectory tool.. backbone
> is off in both cases ...when protein1 is selected and atom select is BAS
> ,the error is : atom select cannot parse selection text
>
> and when protein is selected and atom select is BAS , the error is : no
> atoms selected
>
> On Mon, Dec 11, 2017 at 12:03 PM, Shahee Islam <shaheeislam726_at_gmail.com>
> wrote:
>
>> yes i have checked th bacbone and also for the bead name e.g BAS.still
>> giving the same error: atom select cannot parse selection text
>>
>> On Mon, Dec 11, 2017 at 11:34 AM, Shahee Islam <shaheeislam726_at_gmail.com>
>> wrote:
>>
>>> thank you so much for your reply and i am really so sorry for my late
>>> reply.basically i have two same protein system.i made this system according
>>> to rbcg tutorial using martini force field.i am anlysing rmsd using vmd in
>>> built rmsd trajectory.first i upload psf and then the dcd.after this
>>> selecting backbone allign the system.then click rmsd.
>>> the error is measure fit: no atoms selected.
>>> the segname of my systems are ION,P1,P2,WT1,WT2.
>>>
>>> when i made equvalent atom on and select atom BAS,still i have obtained
>>> the same erorr.
>>>
>>> On Fri, Dec 8, 2017 at 11:24 PM, Peter Freddolino <petefred_at_umich.edu>
>>> wrote:
>>>
>>>> Ok, so what atom selections are you using?
>>>>
>>>> On Fri, Dec 8, 2017 at 9:22 AM, Shahee Islam <shaheeislam726_at_gmail.com>
>>>> wrote:
>>>>
>>>>> Thank you so much for your reply.i want to calculate the rmsd of
>>>>> backbone.And Still when I try to recentering the coarse grained proteins
>>>>> ,the atoms are not selecting.
>>>>>
>>>>> On Dec 8, 2017 7:29 PM, "Peter Freddolino" <petefred_at_umich.edu> wrote:
>>>>>
>>>>>> You would need to send much more information on how you're trying to
>>>>>> calculate the RMSD. My wild guess is that you're looking for alpha carbon
>>>>>> or recognizable backbone atoms when none exist.
>>>>>>
>>>>>> On Fri, Dec 8, 2017 at 3:33 AM, Shahee Islam <
>>>>>> shaheeislam726_at_gmail.com> wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>> i have prepared my system according to rbcg tutorial.Now i want to
>>>>>>> analyse my system by vmd,but during the analysis(rmsd) atoms are not
>>>>>>> selected and also in the time of recentering of proteins.Can anyone please
>>>>>>> help me why this is happening.
>>>>>>> Also i want to know is there any other method to analyse the coarse
>>>>>>> grained system(which is made according to rbcg tutorial).
>>>>>>>
>>>>>>> Thankig you
>>>>>>> Shahee Islam
>>>>>>> University of calcutta
>>>>>>> Department of chemistry
>>>>>>>
>>>>>>
>>>>>>
>>>>
>>>
>>
>

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