On Aug 6, 2014, at 11:27 AM, Sarah Witzke <witzke.sdu.dk> wrote:
> Dear Mark,
>
> Oh yeah - I should be more careful when reading the mails ;-) Sorry, I get it now.
> So, what I do for my systems to get the inpcrd and prmtop files:
> 1) Do whatever the modifications in VMD
> 2) Change the xplor-type psf file to a charmm type psf file with a tcl script like this:
>
> xplor2charmm.psf:
> ****
> package require psfgen
> topology charmm_all36_280813.top
> resetpsf
> readpsf xplor.psf
> writepsf charmm charmm.psf
> exit
> ****
>
> I run the script with "vmd -dispdev text -e xplor2charmm.tcl > xplor2charmm.out".
>
> 3) Insert a line of:
> 0 0 !NUMLP NUMLPH
>
> If you have no cmap term, then this line should be inserted at the end of the .psf file.
> If you do have cmap terms, then this section should only be the second last section.
> For example here is the last few lines of a psf file with cmap terms (!NCRTERM):
>
> ***
> 1 0 !NGRP
> 0 0 0
>
> 0 0 !NUMLP NUMLPH
>
>
> 3 !NCRTERM: cross-terms
> 56 216 218 224 216 218 224 229
> 239 241 243 261 241 243 261 263
> 261 263 265 271 263 265 271 276
> ****
>
> 4) Run chamber (maybe ParmEd now)
>
> I always have to manually insert the section with !NUMLP when using psf files from vmd in chamber.
> Whether there is an easier way to do it, I don't know, but maybe this can help you too?
This is a very thorough set of instructions, thank you. I am _hopeful_ at this point that both chamber and the new ParmEd can correctly parse VMD-generated PSF files (either the XPLOR or CHARMM format) without these superfluous sections you used to have to add. Past versions of chamber were indeed far more picky about the exact format of the PSF.
It would be great to know if the simplified workflow indeed works (and if it doesn't, I think we would consider it a bug to be fixed).
Thanks!
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Aug 06 2014 - 09:30:04 PDT
