Re: atom selection error

From: Shahee Islam (
Date: Mon Dec 11 2017 - 00:04:47 CST

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 <>

> 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

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