From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Aug 07 2010 - 13:10:15 CDT
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.
cheers,
axel.
> Mert
>
> 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
>>
>> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/3209.html
>>
>> 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?
>>
>> Best,
>> Mert
>>
>>
>
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://sites.google.com/site/akohlmey/ Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.
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