From: Mert Gür (gurmert_at_gmail.com)
Date: Sun Aug 08 2010 - 17:07:56 CDT
I am not using any water molecules from the pdb file but your e-mail
and the link were very informative.
I really found a couple of different looking water molecules.
You said that
> To reformulate my question in the light of the information you have provided?
> How does a water molecule of that kind slip into my psf file?
i don't know. you have to track down which files and scripts
you have used to build your final .psf file. it is impossible to
tell from remote where this has happened. i would be very
careful to check it, as there is a finite chance, that something
else might be wrong.
I agree that there can be always something wrong. But why just for a
couple of water molecules which are far away from the protein. That is
what I don't understand.
If the script was doing something wrong shouldn't be all water
On Sun, Aug 8, 2010 at 3:13 AM, felmerino_at_uchile.cl <felmerino_at_uchile.cl> wrote:
> The problem is with the construction of the psf itself. The TIP3 water model
> in the charmm topology file includes the extra bond together with
> an explicit definition of the angle between the oxygen and the hydrogens.
> That way, if you want to use waters from the pdb you have to
> tell vmd "auto none" in the psf builder so it won't generate any angle.
> On the other hand the waters from the solvate plugin come without the exta
> bond so they do not look like triangles (as opposed to those with the
> auto none option).
> It has been discussed some times in the list though
> Take a look here
> ----Mensaje original----
> De: gurmert_at_gmail.com
> Fecha: 07-08-2010 11:20
> Para: "NAMD list"<namd-l_at_ks.uiuc.edu>
> Asunto: namd-l: Reason of FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR
> HT HT OT
> Dear all,
> I am trying to perform MD on CI2 (1YPA.pdb).
> I was getting the following error
> "Warning: Ignored 1 bonds with zero force constants.
> Warning: Will get H-H distance in rigid H2O from H-O-H angle.
> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT"
> I did the modification which is given in the following topic and it worked
> BOND OH2 H1 OH2 H2 H1 H2 ==> BOND OH2 H1 OH2 H2
> Since last year I am using the same topology file for all my MD runs .
> I had never came across with this error.
> What might be the reason for this topology file related error to happen?
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