From: Shahee Islam (shaheeislam726_at_gmail.com)
Date: Mon Dec 11 2017 - 00:52:18 CST
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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