VMD-L Mailing List

From: Paweł Kędzierski (pawel.kedzierski_at_pwr.edu.pl)
Date: Wed Jul 14 2021 - 04:30:29 CDT

W dniu 14.07.2021 o 09:00, Stefan Ivanov pisze:
> Dear VMD users,
>
> I want to load a PDB that has multiple states that have different
> numbers of atoms. The atoms are, in fact, pseudoatoms, so the first
> error I came across was "Exceeded maximum number of bonds (12)." I
> found a workaround in an old post on the mailing list:
>
> https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/14220.html
>
> However, when I load the pdb, I only see one frame, rather then the
> real number of frames in the multimodel PDB.

VMD will not read models differing in the number or atoms. You will have
to split your PDB file into separate files, one for every state, and
load them as separate molecules. If you work on Unix, you can do this
using awk (but copy&paste in any text editor is enough):

awk '/^ENDMDL/{n++};/^(ATOM|HETATM)/{out=sprintf("state_%3d.pdb", n+1); print >> out}' your_multimodel_file.pdb

In VMD terminal, the separate files can be easily loaded all at once in
a loop like this:

foreach state [glob state_*.pdb] {mol new $state}

Then you can use two plugins to achieve what you want, one for cloning
the representations from one molecule to all the others and another for
multi molecule animation to step from one state to another. See this email:

http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/33024.html

Good luck,

Pawel

> I believe this is because the different models have different
> structures which have different numbers of atoms. This is probably a
> contingency VMD was not designed to handle. The different structures
> are not made up of real atoms even but pseudoatoms. I would like to be
> able to examine them using the slider, going through the structures
> one by one. Is this currently possible to do in VMD? I found an old
> post asking a similar question but no concrete asnswer.
>
> _https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/11277.html_
>
> Best wishes,
>
> Stef
> <https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/14220.html>
>
> ERROR) MolAtom 1025: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 1026: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 1027: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 1028: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 1025: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 1026: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 763: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 754: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 764: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 765: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 766: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 767: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 768: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 769: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 770: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 404: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 378: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 389: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 390: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 391: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 291: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 292: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 293: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 295: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 275: Exceeded maximum number of bonds (12).
>