From: Shahee Islam (shaheeislam726_at_gmail.com)
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
On Fri, Dec 8, 2017 at 11:24 PM, Peter Freddolino <petefred_at_umich.edu>
> Ok, so what atom selections are you using?
> On Fri, Dec 8, 2017 at 9:22 AM, Shahee Islam <shaheeislam726_at_gmail.com>
>> 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>
>>>> 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