[gmx-users] grompp problem

[Tom Lenaerts]

>Tom,
>
>Now before anything else..., do you need a CB to be defined? Doesn't
>one of the atom types present suffice? There's tyrosine in most force
>field already, you know, and these 'CB' atoms are merely part of the
>ring.

Indeed.  If I just replace the CB and CR61 by C in the rtp file
and add the bondtypes using the G53a6bon.itp then PTR is defined as follows

[ PTR ]
 [ atoms ] 
; name   type    charge    chargegroup
   O2P    OA    -1.099       1
     P     P     1.162       1 
   O3P    OA    -1.099       1
   O1P    OM    -0.786       1
    OH    OA    -0.178       1
    CZ     C     0.077       2
   CE2     C    -0.038       2
   CD2     C    -0.039       2
   CE1     C    -0.029       3
   CD1     C    -0.029       3
    CG     C     0.002       3
    CB   CH2     0.056       3
    CA   CH1     0.184       4
     C     C     0.436       4
     O     O    -0.546       4
     N    NL     0.835       4

 [ bonds ]
   O2P    P   gb_28  
     P  O3P   gb_28
     P  O1P   gb_24
     P   OH   gb_28
    OH   CZ   gb_13
    CZ  CE2   gb_16
    CZ  CE1   gb_16
   CE2  CD2   gb_16
   CD2   CG   gb_16
   CE1  CD1   gb_16
   CD1   CG   gb_16
    CG   CB   gb_27
    CB   CA   gb_27
    CA    C   gb_27
    CA    N   gb_21 
     C    O   gb_5
                             

Then I get again an error for the command

-bash-3.00$ grompp -f em.mdp -c sh2_pep_b4em.gro -p sh2_pep.top -o sh2_pep.tpr


Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
checking input for internal consistency...
calling /usr/bin/cpp...
processing topology...
Generated 165 of the 1596 non-bonded parameter combinations
WARNING 1 [file "sh2_pep.top", line 2378]:
  No default G96Bond types, using zeroes
WARNING 2 [file "sh2_pep.top", line 2379]:
  No default G96Bond types, using zeroes
WARNING 3 [file "sh2_pep.top", line 2380]:
  No default G96Bond types, using zeroes
WARNING 4 [file "sh2_pep.top", line 2381]:
  No default G96Bond types, using zeroes
WARNING 5 [file "sh2_pep.top", line 2382]:
  No default G96Bond types, using zeroes
WARNING 6 [file "sh2_pep.top", line 2383]:
  No default G96Bond types, using zeroes
WARNING 7 [file "sh2_pep.top", line 2384]:
  No default G96Bond types, using zeroes
WARNING 8 [file "sh2_pep.top", line 2385]:
  No default G96Bond types, using zeroes
WARNING 9 [file "sh2_pep.top", line 2386]:
  No default G96Bond types, using zeroes
WARNING 10 [file "sh2_pep.top", line 2387]:
  No default G96Bond types, using zeroes
Cleaning up temporary file grompp6oaBPr
-------------------------------------------------------
Program grompp, VERSION 3.3
Source code file: fatal.c, line: 416

Fatal error:
Too many warnings, grompp terminated
-------------------------------------------------------

"It's Because Of the Metric System" (Pulp Fiction)