Re: atom selection error

From: Shahee Islam (shaheeislam726_at_gmail.com)
Date: Mon Dec 11 2017 - 00:33:38 CST

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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