[gmx-users] Still "GB parameter(s) missing or negative for atom type 'C'" issue after 7 years

[Vedat Durmaz]

Sorry, typo: "I can NOT get my system grompped" ...


Am 28.08.19 um 12:03 schrieb Vedat Durmaz:
> Hi everybody,
>
>
> After 7 years I'm trying to do some implicit solvent simulations of
> protein-ligand systems again using Gromacs/Amber and running into the
> same issue as before:
>
> GB parameter(s) missing or negative for atom type 'N3'
> GB parameter(s) missing or negative for atom type 'H'
> GB parameter(s) missing or negative for atom type 'CT'
> GB parameter(s) missing or negative for atom type 'HP'
> GB parameter(s) missing or negative for atom type 'HC'
> GB parameter(s) missing or negative for atom type 'H1'
> GB parameter(s) missing or negative for atom type 'S'
> GB parameter(s) missing or negative for atom type 'C'
> GB parameter(s) missing or negative for atom type 'O'
> GB parameter(s) missing or negative for atom type 'HA'
> GB parameter(s) missing or negative for atom type 'OH'
> GB parameter(s) missing or negative for atom type 'HO'
> GB parameter(s) missing or negative for atom type 'OS' 
>
> Can't do GB electrostatics; the implicit_genborn_params section of the
> forcefield is missing parameters for 13 atomtypes or they might be negative.
>
> I googled the problem and found a discussion from 2012, which
> surprisingly was initialized by myself running into the same issue!  xD
>
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-May/071102.html
>
> And just as in 2012, I can get my system grompped, although these atom
> types listed above are in the force field's gbsa.itp file (apart from
> the ether oxygen OS which I added manually as a copy of the carbonyl
> atom type "O". Some info:
>
>
> ## My top file:
>
> #include "amber99sb-ildn.ff/forcefield.itp"
> #include "ligand.itp"
> #include "protein.itp"
>
>
> ## My atom types section at the top of the ligand.itp file:
>
> [ atomtypes ]
> ;name   bond_type     mass     charge   ptype   sigma        
> epsilon       Amb
>  CT       CT          0.00000  0.00000   A     3.39967e-01   4.57730e-01
> ; 1.91  0.1094
>  HP       HP          0.00000  0.00000   A     1.95998e-01   6.56888e-02
> ; 1.10  0.0157
>  H1       H1          0.00000  0.00000   A     2.47135e-01   6.56888e-02
> ; 1.39  0.0157
>  HC       HC          0.00000  0.00000   A     2.64953e-01   6.56888e-02
> ; 1.49  0.0157
>  S        S           0.00000  0.00000   A     3.56359e-01   1.04600e+00
> ; 2.00  0.2500
>  C        C           0.00000  0.00000   A     3.39967e-01   3.59824e-01
> ; 1.91  0.0860
>  O        O           0.00000  0.00000   A     2.95992e-01   8.78640e-01
> ; 1.66  0.2100
>  N3       N3          0.00000  0.00000   A     3.25000e-01   7.11280e-01
> ; 1.82  0.1700
>  H        H           0.00000  0.00000   A     1.06908e-01   6.56888e-02
> ; 0.60  0.0157
>  N        N           0.00000  0.00000   A     3.25000e-01   7.11280e-01
> ; 1.82  0.1700
>  O2       O2          0.00000  0.00000   A     2.95992e-01   8.78640e-01
> ; 1.66  0.2100
>  CD       CD          0.00000  0.00000   A     3.39967e-01   3.59824e-01
> ; 1.91  0.0860
>  OH       OH          0.00000  0.00000   A     3.06647e-01   8.80314e-01
> ; 1.72  0.2104
>  HO       HO          0.00000  0.00000   A     0.00000e+00   0.00000e+00
> ; 0.00  0.0000
>  CM       CM          0.00000  0.00000   A     3.39967e-01   3.59824e-01
> ; 1.91  0.0860
>  HA       HA          0.00000  0.00000   A     2.59964e-01   6.27600e-02
> ; 1.46  0.0150
>  OS       OS          0.00000  0.00000   A     3.00001e-01   7.11280e-01
> ; 1.68  0.1700
>
> Did ever anyone find a solution for that issue?
>
> Many thanks!
>
> Vedat
>
>
>