Re: renumbering and rewriting a trajectory

From: Kodituwakku,Dimuthu Nirmani (
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?


From: Ren Hafner TUK <>
Sent: Wednesday, September 30, 2020 11:41 AM
To: <>; Kodituwakku,Dimuthu Nirmani <>
Subject: Re: namd-l: renumbering and rewriting a trajectory

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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.



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,

Dipl.-Phys. Ren Hafner
TU Kaiserslautern

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