Re: Reason of FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT

From: felmerino_at_uchile.cl
Date: Sat Aug 07 2010 - 19:13:59 CDT

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

http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/2666.html

best

Felipe

----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

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

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