From: Maximilian Ebert (max.ebert_at_me.com)
Date: Fri Jun 04 2021 - 13:51:49 CDT
Thanks for the answer. I am trying to write out a compliment PSF file for system with over 1 million atoms. I want to be sure to not bust any field width and get into trouble with the NAMD PSF parser. So I guess you can’t be fully compliant for system which go over a certain number of atoms correct? Is my assumption correct that NAMD uses the space as a separator and that VMD for example has fixed field width?
Max
> On Jun 4, 2021, at 1:59 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>
> lore has it that the *authoritative* documentation of the CHARMM file formats is the CHARMM source code.
>
> one important point to note is that PSF (and PDB) are file formats based on Fortran style formatting, which has fixed widths and does not need spaces as separators.
> so it can be legal to have something like:
>
> 1001100210031004 (for a 4I4 format) being read as 1001, 1002, 1003, 1004 but if you would write out 1001 1002 1003 1004 in would be read as 1001, 100, 210, 31
> that is different from how C/C++ and Python process input.
>
> So what it now boils down to is what you are after: do you want to write out or edit PSF files to be fully conforming, or do they just have to be read by NAMD.
>
> Axel.
>
> P.S.: there are some more possible flags to appear in the first line to indicate the use of the PSF for specific purposes
>
>
> On Fri, Jun 4, 2021 at 1:49 PM Josh Vermaas <vermaasj_at_msu.edu <mailto:vermaasj_at_msu.edu>> wrote:
> The best documentation on the format is *probably* the CHARMM
> documentation, which is actually rather sparse.
> https://urldefense.com/v3/__https://academiccharmm.org/documentation/version/c45b2/io*IOFORM__;Iw!!DZ3fjg!uRPWqMKGW1780p7gOxom55ZPP9L4h9AHLa2pb7HsKx66nLOh7NH4vymgTxHM9_y3qw$ <https://urldefense.com/v3/__https://academiccharmm.org/documentation/version/c45b2/io*IOFORM__;Iw!!DZ3fjg!uRPWqMKGW1780p7gOxom55ZPP9L4h9AHLa2pb7HsKx66nLOh7NH4vymgTxHM9_y3qw$>
>
> Basically, the first line of the PSF file dictates the field width. For
> regular, non-extended PSFs, the header will look like:
>
> PSF
>
> In these files, you are limited to 4 characters for segnames and
> atomtypes. CHARMM can also write (and VMD/NAMD can also read/write)
> "extended" PSF files. The headers for these will look like:
>
> PSF EXT
>
> This buys you 8 characters for segnames and atomtypes. NAMD/VMD also can
> write space-delimited psf files, which are tagged as follows:
>
> PSF NAMD
>
> The NAMD/VMD version is the most flexible, since fields just need to be
> separated by spaces, and for the most part psfgen/VMD will select this
> option if the contents of the psf file demand it.
>
> -Josh
>
> On 6/4/21 1:10 PM, Maximilian Ebert wrote:
> > Dear list,
> >
> > Is there a resource which describes the PSF file format? I am many wondering about the max column width and if the width needs to be fixed or can changed when numbers get larger.
> >
> > Thanks
> >
> --
> Josh Vermaas
>
> vermaasj_at_msu.edu <mailto:vermaasj_at_msu.edu>
> Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
> Michigan State University
> https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!uRPWqMKGW1780p7gOxom55ZPP9L4h9AHLa2pb7HsKx66nLOh7NH4vymgTxF1980Jig$ <https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!uRPWqMKGW1780p7gOxom55ZPP9L4h9AHLa2pb7HsKx66nLOh7NH4vymgTxF1980Jig$>
>
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com <mailto:akohlmey_at_gmail.com> https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!rEJu6_H8cDKYNH3kS6pdPBlDfMIMi7LjGo_8KKGxFUzUh-nlF9KJXxO51I66IS-5Rw$ <https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!rEJu6_H8cDKYNH3kS6pdPBlDfMIMi7LjGo_8KKGxFUzUh-nlF9KJXxO51I66IS-5Rw$ >
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
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