VMD-L Mailing List

From: Stefan Ivanov (bindqgodzgun_at_abv.bg)
Date: Wed Jul 14 2021 - 02:00:24 CDT

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. 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
  

  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).