Re: renumbering and rewriting a trajectory

From: René Hafner TUK (hamburge_at_physik.uni-kl.de)
Date: Mon Oct 05 2020 - 10:30:54 CDT

Hi Dimuthu,

Idk. Did you change the psf by coding or by hand? Then you might have
misaligned something.
The code should be:

Load your psf.

Then load dcd.

Apply your code below to renumber resids.

save psf via writepsf and an atomselection containing all of the atoms.

load just saved psf as molecule.

load dcd into newly loaded psf.

check the structure.

if it still does not work you can sent it to me then I can have a look.

Cheers

Ren

On 10/4/2020 5:12 AM, Kodituwakku,Dimuthu Nirmani wrote:
> 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 somethingwrong?
>
> 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

-- 
--
Dipl.-Phys. Ren Hafner
TU Kaiserslautern
Germany

This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:10 CST