Hi Dan,
Sorry for getting back to you later. We have just come back from a summer
vacation.
Thank you for responding.
"I'm certain there is no bug"
Yes you are right. I have noticed a glitch in our Linux server. I have
recently noticed that I used a linux editor that adds "^M" at the end of
each line. I also found a swap file in the directory I was running cpptraj,
which defines alpha torsion as
:n.O3' :n.P :n.O5' :n.C5'
I remember, I had edited this file to redefine alpha torsion as
:n-1.O3' :n.P :n.O5' :n.C5'
Even though I used the edited file as input in cpptraj many times, I kept
getting the same weird results for the alpha torsions as before.
I have recently generated a new cpptraj input file in a different directory
using the correct definition of the alpha torsion, and the result came out
to be alright, giving rise to major populations for gauche - . So, it works
now :)
Well, I have decided to upgrade and reinstall Linux OS on the server.
Problem is solved.
Thank you for your suggestions on troubleshooting.
Best regards,
Cenk
On Wed, Aug 24, 2022 at 5:43 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Fri, Aug 19, 2022 at 4:23 PM Cenk Andac <cenkandac.gmail.com> wrote:
> > I have an MD trajectory for A-RNA double helix. I have gone through may
> of the frames and computed alpha torsions manually via UCSF Chimera, they
> are all around ~ 60o (gauche -).
>
> Again, ~ 60 deg. is gauche +, not gauche -.
>
> >
> > Having said that I now am quite confused with the stat output I
> previously mentioned. It says the average alpha torsion is around +60o
> while I manually measured -60o (minus for counterclockwise torsions)
>
> Without knowing exactly how you manually measured these torsions I
> have no idea. Maybe you used different atoms, or had them in a
> different order - I can only guess. All this is to say I'm certain
> there is no bug in either the 'dihedral' action or the 'stat'
> analysis. Also keep in mind that just because a dihedral usually
> adopts certain values, that doesn't necessarily mean it can't adopt
> other values (as Ilyas has been indicating). Hope this was helpful,
>
> -Dan
>
> >
> > Do you have any idea as to what I am missing here!!
> >
> > Best,
> >
> > Cenk
> >
> >
> > On Fri, Aug 19, 2022, 5:30 PM Daniel Roe via AMBER <amber.ambermd.org>
> wrote:
> >>
> >> Hi,
> >>
> >> On Fri, Aug 19, 2022 at 3:32 AM Cenk Andac via AMBER <amber.ambermd.org>
> wrote:
> >> >
> >> > STATISTICS G2-alpha
> >> > AVERAGE: 65.8043 (10.0676 stddev)
> >> > INITIAL: 64.6928
> >> > FINAL: 57.9292
> >>
> >> A torsion value of 65 deg. is almost right in the middle of what by
> >> convention is considered gauche+ (between 30 and 90 degrees), so
> >> everything seems correct. Why do you think this is a bug?
> >>
> >> -Dan
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Sep 03 2022 - 07:30:02 PDT
