From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Aug 07 2010 - 15:28:29 CDT
On Sat, Aug 7, 2010 at 4:12 PM, Mert Gür <gurmert_at_gmail.com> wrote:
> Dear Axel,
> 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).
the source of the problem is not from running namd,
but from generating the .psf file.
> 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 thought that all generated TIP3 waters are the same. But you are
no. it depends on which software and what inputs you use
to build the psf file.
> saying that there are water molecules with 3 bond and 2 bonds present
> in my psf file.
you can use VMD to visually inspect your files. if you get lucky,
you'll see it right away. if not, you have to be a bit creative.
remember: software is dumb and does _exactly_ what it is
programmed to do. sometimes that can work against you.
cheers,
axel.
> Best,
> Mert
>
>
> 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.
>>
>> 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.
>>
>
-- 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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