[gmx-users] grompp and [ ?types ]

[David L. Bostick]

Ok, I take back part of the previous message.  If I add the angles
manually, grompp doesn't find the error, however, these angles are standard
in in the ffgmx files.  Is there any reason that grompp might not recognize
them in these particular residues?  (NAC, ACE)  

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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On Fri, 19 Apr 2002, David L. Bostick wrote:

> 
> 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
> 
> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
> 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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