On Mon, Sep 15, 2014 at 6:47 PM, Sarah Witzke <witzke.sdu.dk> wrote:
> Hi Eric,
>
> I had a quick look at your attached files.
> For me, the problem with your .psf file is the xplor "atom reference
> numbers" (or what they are correctly called) for TIP3P:
>
> >From your .psf file:
> 73 WC 8013 TIP3 OH2 75 -0.834000 15.9994 0
> 74 WC 8013 TIP3 H1 4 0.417000 1.0080 0
> 75 WC 8013 TIP3 H2 4 0.417000 1.0080 0
>
> >From a new version of the .psf file:
> 73 W 8013 TIP3 OH2 3 -0.834000 15.9994 0
> 74 W 8013 TIP3 H1 1 0.417000 1.0080 0
> 75 W 8013 TIP3 H2 1 0.417000 1.0080 0
>
> Notice 75,4,4 vs. 3,1,1.
>
> Do you use the same topology file for TIP3P for when you use psfgen to get
> the .psf files as when you run chamber?
>
> I have made new pdf files (both charmm and xplor type) and have run them
> successful through chamber in ParmEd.
>
Thanks for hunting this down! The error messages when chamber fails in
ParmEd are garbage right now. I will fix that.
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Sep 15 2014 - 18:30:02 PDT
