[gmx-users] grompp and [ ?types ]

[David L. Bostick]

Hi Erik,

The original entry  for the GLU from the original PDB file that becomes
GLUH after pdb2gmx is:
ATOM   1544  N   GLU   235      87.687  40.544  16.986  1.00 80.74
ATOM   1545  CA  GLU   235      87.395  40.535  15.564  1.00 84.24
ATOM   1546  C   GLU   235      86.875  39.183  15.064  1.00 86.12
ATOM   1547  O   GLU   235      85.770  39.098  14.523  1.00 87.14
ATOM   1548  CB  GLU   235      88.645  40.908  14.772  1.00 87.92
ATOM   1549  CG  GLU   235      89.234  42.276  15.070  1.00 99.37
ATOM   1550  CD  GLU   235      90.506  42.517  14.263  1.00112.58
ATOM   1551  OE1 GLU   235      90.418  42.566  13.015  1.00113.76
ATOM   1552  OE2 GLU   235      91.596  42.636  14.871  1.00115.15

After pdb2gmx, the portion of the .itp covering atom types is:
  3158      N    206   GLUH      N   1212      -0.28    14.0067 
  3159      H    206   GLUH      H   1212       0.28      1.008  
  3160     C1    206   GLUH     CA   1213          0     12.011 
  3161     HC    206   GLUH     HA   1213          0      1.008  
  3162     C2    206   GLUH     CB   1214          0     12.011 
  3163     HC    206   GLUH    HB1   1214          0      1.008  
  3164     HC    206   GLUH    HB2   1214          0      1.008  
  3165     C2    206   GLUH     CG   1215          0     12.011 
  3166     HC    206   GLUH    HG1   1215          0      1.008 
  3167     HC    206   GLUH    HG2   1215          0      1.008  
  3168      C    206   GLUH     CD   1216       0.53     12.011  
  3169      O    206   GLUH    OE1   1216      -0.38    15.9994
  3170     OA    206   GLUH    OE2   1216     -0.548    15.9994
  3171     HO    206   GLUH    HE2   1216      0.398      1.008  
  3172      C    206   GLUH      C   1217       0.38     12.011 
  3173      O    206   GLUH      O   1217      -0.38    15.9994

This residue actually, gave a dihedraltypes warning:
---------------------------------------------------------
WARNING 6 [file
"//alberto/programs/gmx_development/gmx-bin/share/clc_force_top/clcA.itp",
line 42784]:
  No default Improper Dih. types, using zeroes
--------------------------------------------------------
Line 42784 of the itp file is:

 3158  3160  3162  3172     2

which corresponds to the improper dihedraltype N-C1-C2-C, and can be found
in both ffgmx.itp and ffgmx2.itp as:

    C    N    1   180.000      33.472      2 




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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	
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-

On Fri, 19 Apr 2002, Erik Lindahl wrote:

> 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.
> >
> 
> Hi David,
> 
> I suspect it has something to do with the atom naming...
> Could you post the atom lines of those residues from the PDB file?  (One 
> GLUH will do)
> 
> Cheers,
> 
> Erik
> 
> 
> 
> 
> 
> 
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