From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Wed Dec 17 2003 - 09:23:02 CST
OK,
Looking at your energies, I see that ANGLE and DIHEDRAL are zero. Looking
at your psf file shows that there are no angles or dihedrals listed.
In your psfgen script you have this:
segment C {
auto none
first none
last none
pdb chainC.pdb
}
That "auto none" means "don't autogenerate angles or dihedrals". You need
to specify "auto none" for segments of water, but keep the default of
"auto angles dihedrals" specified in the topology file for proteins,
lipids, nucleic acids, etc.
-Jim
On Wed, 17 Dec 2003, Gadi Oron wrote:
> Hi again, and a big thank-you for those who look into my problem...
>
> On Wed, 2003-12-17 at 06:10, Jim Phillips wrote:
>
> > Hi,
> >
> > It looks like this is your problem:
> >
> > unknown patch type PT1
> > ERROR: failed to apply patch
>
>
>
> > I think you meant to type TP1. If you do, you get:
> > applying patch TP1 to 1 residues
> > unknown atom type ON3
> > add atom failed in patch TP1
> > ERROR: failed to apply patch
> > If I substitute the prot_na topology file for prot_lipid there are other
> > atom types missing, but if you include them both then psfgen is happy.
> >
> > Hopefully this will fix your minimization problems.
>
>
>
> Thank you for the info, it is really useful. As pointed by Alex, I
> should really take a more careful look at the psfgen output, and insist
> that everything is going smoothly.
>
> You are right that the patches I use cause some mayhem, but I believe
> that this is not the cause for the crashes. The proof for that is the
> fact that I cannot simulate a single chain from the structure I have
> shown, not using any patches and passing psfgen with no errors, and
> still get the same behavior!
>
> To illustrate it, I have prepared a file located HERE. It reproduces the
> same crash, while psfgen passes with only a warning on badly guessed
> coordinates (should this considered an issue?).
>
> To use this file, extract, use psfgen < stepC.psfgen, then run
> ./run_namd.sh equil.namd.
>
> The MD will crash after 20 simulation steps. But take a look at the
> Arginines during the minimization, they become strangely distorted with
> atoms as close as 0.1 A (!!).
>
> Any idea someone?
>
> Best regards.
>
> --
> ================= Gadi ORON, PhD -o- Proteologics ======================
> =========== gadi/at/proteologics.com =========== +972 8 9475666 ===========
> A prediction is worth twenty explanations.
> -- K. Brecher
>
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