From: Mert Gür (gurmert_at_gmail.com)
Date: Sat Aug 07 2010 - 15:12:15 CDT
Thanks for the explanation. However, I have read the explanation and
the only difference between the other 5 systems and this system are
the proteins (topology file used and namd versions are the same).
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 thought that all generated TIP3 waters are the same. But you are
saying that there are water molecules with 3 bond and 2 bonds present
in my psf file.
On Sat, Aug 7, 2010 at 9:10 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Sat, Aug 7, 2010 at 12:39 PM, Mert Gür <gurmert_at_gmail.com> wrote:
>> I mean it didn't happen for the other 5 proteins. Why did it happen
>> for this one.
> i suggest your read peter's explanation at the bottom of
> the mail that you linked to.
> the problem is in water and not the protein. if the psf
> file has an H-H bond for a water molecule and is lacking
> the angle definition instead, you get this behavior. some
> classical MD programs keep water molecules rigid by
> defining them to be a triangle of 3 bonds.
> obviously, a water molecule of that kind slipped into your .psf.
>> On Sat, Aug 7, 2010 at 6:20 PM, Mert Gür <gurmert_at_gmail.com> wrote:
>>> 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?
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
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