Re: atom selection error

From: Peter Freddolino (
Date: Mon Dec 11 2017 - 00:38:19 CST

Please try to clarify your problem. Two emails ago, you mentioned the error
"no atoms selected." Now you are saying it is "atom select cannot parse
selection text". This is not the same error!
Also, I think you may have misinterpreted my previous email. My point is
that backbone should *not* be checked.

On Mon, Dec 11, 2017 at 1:33 AM, Shahee Islam <>

> 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 <>
> 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 <>
>> wrote:
>>> Ok, so what atom selections are you using?
>>> On Fri, Dec 8, 2017 at 9:22 AM, Shahee Islam <>
>>> 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" <> 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 <
>>>>> > 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

This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:21:49 CST