Good afternoon,
Jason's explanation makes perfect sense and solves the problem. I
apologize for not understanding that upon stripping that there is a
renumbering of the residues. Dan's very elegant solution of adding a
semicolon spared me from having to even do some arithmetic in my head to
renumber things :)
The cpptraj script thus runs without error, producing a requested
principle component. My last question is not AMBER-specific, I do not
believe. When I examine the visualization of the "mode" of largest
variance, I see an extreme lengthening of several bonds in VMD (i.e.,
they look like they are "stretching" to an unphysical degree). I am very
confused why this could happen, short of user error. Is it for some
reason "normal" to see that the highest variance in positions between
"bonded" atoms could be large, as in visually stretched a huge degree? I
assume not, and that this is an error somewhere on my part, but I wanted
to check if I have a misunderstanding before I go back to the drawing board.
On 8/21/18 9:39 AM, Daniel Roe wrote:
> Hi,
>
> On Mon, Aug 20, 2018 at 10:54 PM Jason Swails <jason.swails.gmail.com> wrote:
>> You have stripped out residues 1-37 and 319-<total number of residues>.
>> You now have 244 residues left (it seems that your system doesn't have 318
>> full residues? I would have expected 281 left if it did). These are now
>> residues 1-244 since cpptraj always numbers residues from 1.
> Jason's explanation is spot-on (as usual).
>
> Note that in recent versions of CPPTRAJ you can now use the ':;'
> (colon semicolon) token to use original residue numbers (even after
> stripping the system), e.g.
>
> :;38-318&!.H=
>
> This may be more intuitive. Hope this helps,
>
> -Dan
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr. Robert Molt Jr.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 21 2018 - 09:30:02 PDT
