From: Brian Radak (brian.radak_at_gmail.com)
Date: Mon Dec 11 2017 - 11:14:36 CST
A lot of the shorthand selection syntax like "protein" "nucleic",
"sidechain", and "backbone" are based on heuristics with the residue and
atom names - an adventurous user could probably find these in the source
code.
I would make your selection explicitly, since Martini probably breaks
the heuristics.
HTH,
BKR
On 12/11/2017 01:24 AM, Peter Freddolino wrote:
> Do you still have backbone checked? The CG backbone beads don't count
> as backbone for vmd's atom selections...
>
> On Mon, Dec 11, 2017 at 1:04 AM, Shahee Islam
> <shaheeislam726_at_gmail.com <mailto: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 <mailto: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 <mailto: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 <mailto: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
> <mailto: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
>
>
>
>
>
This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:21:50 CST