[gmx-users] grompp and [ ?types ]

[David L. Bostick]

Hello all,

I just built a topology for a protein.  The termini were capped with ACE at
the N and NAC (N-methyl) at the C.  One of the GLU residues is supposed to
be GLUH.  I used pdb2gmx with all the appropriate options.  However, when
doing a test grompp of the protein, I keep getting these kinds of warnings:

WARNING 1 [file "//alberto/programs/gmx-3.1/share/clc_force_top/clcA.itp",
line 27217]:
  No default Angle types, using zeroes
WARNING 2 [file "//alberto/programs/gmx-3.1/share/clc_force_top/clcA.itp",
line 27219]:
  No default Angle types, using zeroes
WARNING 3 [file "//alberto/programs/gmx-3.1/share/clc_force_top/clcA.itp",
line 27220]:
  No default Angle types, using zeroes

I checked these lines in the .itp files I created using the .top made by
pdb2gmx.  They all coincidentally correspond to parameters in the ACE, NAC,
or GLUH amino acids.  Furthermore, they are standard angletypes.. like

HC C3 HC

I looked for these in ffgmx2bon.itp and they are there.  I also added the
parameters I found in ffgmx2bon.itp for these angles and I still get the
error.  Why doesn't grompp find these in the .itp files it searches.

David

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David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165 
Program in Molecular and Cellular Biophysics 
UNC-Chapel Hill					
CB #3255 Phillips Hall				dbostick at physics.unc.edu	
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick	
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