From: Mert Gür (gurmert_at_gmail.com)
Date: Mon Aug 09 2010 - 08:14:39 CDT
I got the answer but I am confused.
I have to thank you because as you said I actually did something
different. I did not call the topology file prior to the solvate
So VMD used its own topology file to generate the waters which I
believe did not fit the the topology file I used for the simulation.
I used the topology file in toppar_c35b2_c36a2/top_all_27_lipid.inp at the link
In VMD's topology file the third angle is commented out as
!BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake
BOND OH2 H1 OH2 H2
ANGLE H1 OH2 H2
whereas in the topology file I used it is not commented out
BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake
ANGLE H1 OH2 H2 ! required
So the problem is that my topology file in NAMD tells NAMD that it
requires ANGLE PARAMETERS FOR HT HT OT to define the H-H bond. Did I
got that right?
However, In the psf file this extra bond between this hydrogen atoms
is not present.
By the way I did not use any rigid bonds in my simulation.
In this topic Peter states that these bond will be generally ignored
by NAMD and doesn't generally appear in the topology files they
So actually NAMD has no problem if we defined or did not defined this
H-H bond. Both topology files work fine .
NAMD will ignore it any way. Is that right?
Hence, I got confused with all these previous discussions . Some say
that it is better to delete it.
But I don't see why.
This H-H bond is also found in Mackerell's topology files.
Is it required to delete this H-H bond or not?
I have obtained many MD simulations without doing so.
On Sat, Aug 7, 2010 at 11:28 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> 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.
>> 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.
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
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