From: Kodituwakku,Dimuthu Nirmani (dkodituwakku_at_ufl.edu)
Date: Sat Oct 03 2020 - 22:12:05 CDT
Hello Hafner,
Thank you for your reply. I wrote a renumbered psf and tried to load the psf along with the dcd file. I see dragged and incorrect bonds. Am I doing something wrong?
Best,
Dimuthu
________________________________
From: Ren Hafner TUK <hamburge_at_physik.uni-kl.de>
Sent: Wednesday, September 30, 2020 11:41 AM
To: namd-l_at_ks.uiuc.edu <namd-l_at_ks.uiuc.edu>; Kodituwakku,Dimuthu Nirmani <dkodituwakku_at_ufl.edu>
Subject: Re: namd-l: renumbering and rewriting a trajectory
[External Email]
Hi,
the resid is not stored in a (dcd) trajectory file but in a PSF file.
Therefore you just need to write out a new PSF file.
Cheers
Ren
On 9/30/2020 5:30 PM, Kodituwakku,Dimuthu Nirmani wrote:
Hi all,
I postprocessed a trajectory by renumbering using the following script (vmd/1.9.3) (which I obtained from a previous post),
for {set ires 1} { $ires <= 587 } { incr ires } {
set a [atomselect top "resid $ires and segid 1GPB"]
set newires [expr $ires + 587]
$a set resid $newires
$a delete
}
But I'm having trouble rewriting the trajectory using "animate" keyword, although it writes the trajectory it doesn't change numbering.
Any help would be appreciated,
Thank you,
Best,
Dimuthu
-- -- Dipl.-Phys. Ren Hafner TU Kaiserslautern Germany
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