Re: atom selection error

From: Shahee Islam (shaheeislam726_at_gmail.com)
Date: Tue Dec 12 2017 - 01:31:22 CST

thank you so much for all of your reply.In vmd inbuilt rmsd
trajectory,first selecting the protein as fragment p1 (or fragment p2),two
proteins are same.then backbone option remain off and selecting atom BAS
(or CA.O.N,C) and then selecting weight on...selecting field as mass and
next clicking allign option and last clicking rmsd,i get the rmsd value.
wheather i select fragment p1 or fragment p2,i am getting the same
value.(this dcd is ended on 807 ns)
Is it correct.

On Tue, Dec 12, 2017 at 1:56 AM, Peter Freddolino <petefred_at_umich.edu>
wrote:

> 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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