[gmx-users] Grompp errors?

[Jones de Andrade]

Hi all!.

I was trying to simulate a complex cation in MeCN solution and I got 2
strange warnings to me:

processing topology...
WARNING 1 [file "ff_emi.itp", line 7]:
  Overriding atomtype CT
WARNING 2 [file "ff_emi.itp", line 11]:
  Overriding atomtype H1

But I did found that strange because, as you can see in the file
attached, the entries CT and H1 are just called once.

A second thing that called my attention is the following line that
grompp gives me: "Generating 1-4 interactions: fudge = 0.5". It's not
wrong, since I put this fudge for the VdW interactions, BUT I also
placed a different fudge for the intramolecular coulombic interations
(0.8333), using these lines in the ".top" file I created:

[ defaults ]
; nbfunc      com-rule    gen-pairs      fudgeLJ  fudgeQ
    1            2          yes           0.5000  0.8333

Shouldn't grompp output two fudge parameters instead of only one?

Are those known issues? I just found those warnings in case of use of
standard force fields, what is not the case. The fudge output I could
not find any possible answer.

Thanks a lot for everything in advance.

Jones
-------------- next part --------------
;
;     emi Force Field Topology File
;
  
[ atomtypes ]
; name  mass (a.m.u.)  charge (e) ptype  sigma (nm)  epsilon (kJ/mol)
  CT    12.0112         0.000     A      0.3400      0.4577
  NA    14.0067         0.000     A      0.3250      0.7113
  CR    12.0112         0.000     A      0.3400      0.3598
  CW    12.0112         0.000     A      0.3400      0.3598
  H1     1.0080         0.000     A      0.2471      0.0657
  HC     1.0080         0.000     A      0.2649      0.0657
  H5     1.0080         0.000     A      0.2421      0.0628
  H4     1.0080         0.000     A      0.2511      0.0628
  
[ bondtypes ]
;  i     j     funct    b0 (nm)      kb (kJ/mol.nm^2)
   CT    NA    1        0.1475       141000.81
   CT    CT    1        0.1526       129704.00
   NA    CR    1        0.1343       199576.80
   NA    CW    1        0.1381       178656.80
   CW    CW    1        0.1350       229701.61
   H1    CT    1        0.1090       142256.00
   HC    CT    1        0.1090       142256.00
   H5    CR    1        0.1080       153552.80
   H4    CW    1        0.1080       153552.80
  
[ angletypes ]
;  i     j     k      funct    th0 (degree)      kb (kJ/mol.rad^2)
   H1    CT    H1     1        109.50            146.44
   H1    CT    NA     1        109.50            209.20
   H1    CT    CT     1        109.50            209.20
   CT    CT    NA     1        109.50            209.20
   HC    CT    HC     1        109.50            146.44
   HC    CT    CT     1        109.50            209.20
   CT    NA    CR     1        128.80            292.88
   CT    NA    CW     1        121.20            292.88
   CR    NA    CW     1        120.00            292.88
   H5    CR    NA     1        120.00            146.44
   NA    CR    NA     1        120.00            292.88
   H4    CW    NA     1        120.00            146.44
   H4    CW    CW     1        119.70            146.44
   NA    CW    CW     1        121.20            292.88
  
[ dihedraltypes ]
;  j     k      funct    phi (degree)      cp (kJ/mol.rad^2)       mult(n)
   CT    NA     1          0.00             0.0000                 2.0
   CT    CT     1          0.00             0.6510                 3.0
   CW    CW     1        180.00            27.8236                 2.0