Re: pdb file from a particular configuration

From: Bunzeki Kilolo (Mme) (
Date: Tue Jun 28 2022 - 04:10:02 CDT

Hello Ribi,

Try ;

bomlev -5
wrnlev 5

stream job.str

open unit 10 read card name structure.psf
read psf xplor card unit 10 append

open unit 4 read card name structure.pdb
read coord pdb unit 4 resid

open read unform unit 22 name traj.dcd
trajectory first 22 nunit 1 begin 1 skip 250

set i 1
set ntot ?nfile

label nextconf

traj read
open write card unit 12 name traj.conf__at_i.pdb
write coor pdb unit 12
close unit 12
incr i by 1

if @i le @ntot goto nextconf



De: "Ribi Akbar" <>
Envoyé: Mardi 28 Juin 2022 09:49:17
Objet: namd-l: pdb file from a particular configuration

I am currently facing a problem when creating a PDB file from the dcd file. Suppose that we have 10000 trajectories, each frame shows a different configuration of the system (MD simulation) and we are interested in the configuration at frame 5000 (MD simulation), is it possible to do this using VMD? Thanks for your attention.

Kind regards,
Ribi Akbar

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