Re: an error when merge pdb and psf files in vmd for big model

From: Chris Harrison (
Date: Sun Sep 09 2012 - 09:16:28 CDT


At 2M atoms, this is most likely happening b/c pdb is a column-delimited
format file. The atom index field runs out of columns.

If you are experiencing problems with 2M atom pdb/psf pairs in namd
(but at 2M atoms, you should still be ok ...) then you could use instead
the js file format.


farzad kiani <> writes:
> Date: Sun, 9 Sep 2012 06:45:58 -0700 (PDT)
> From: farzad kiani <>
> To: "" <>
> Subject: namd-l: an error when merge pdb and psf files in vmd for big model
> Reply-To: farzad kiani <>
> X-Mailer: YahooMailWebService/
> Hi
> I have made a big model. 2000000 atoms in five parts
> I want to merge psf and pdb files. when using merge structures icons in VMD I got an error. in text files for pdb and psf, printed ****** instead atom no.
> can any one help me?
> Thanks a lot
> Kiani 


Chris Harrison, Ph.D.
NIH Center for Macromolecular Modeling and Bioinformatics
Theoretical and Computational Biophysics Group
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801       Voice: 773-570-6078               Fax:   217-244-6078

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