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

Vedat Durmaz vedat.durmaz at gmx.net
Wed Aug 28 17:01:59 CEST 2019


Hi Mark,

Thanks for your hint regarding the order of itp files. I got it running
now.

Here's my solution for all other users (as well as for myself in 7 years
again). I had an ligand itp file generated with "acpype -a amber -i
ligand.pdb" in order to have the upper case atom type notation. At the
top of that itp file, a first section [ atom types ] lists all relevant
atom types.

Some of these types are already included in the amber force field's
gbsa.itp in the corresponding amber force field directory in
gromacs/top. These atom types can be safely removed from the atom types
section of the ligand.itp file. For those atom types of the ligand that
are not listed in gbsa.itp, it was not helpful to use the corresponding
atom type lines from ligand.itp. In my case this resulted in a
segmentation fault.

My work-around was to add these few types to a local copy (important due
to reordering of itp files later!) of gbsa.itp by copying the parameters
from respective atom types already existing in gbsa.itp with most
similar properties (sp2/3, 1/2 membered ring, ring junction, etc.).
Strangely, I additionally needed to keep exactly one of these manually
added atom types in my ligand's atom types section.


Finally, I still had to reorder include lines in my top file in the
following way:

#include "amber99sb-ildn.ff/forcefield.itp"
[ atomtypes ]
;name   bond_type     mass     charge   ptype   sigma        
epsilon       Amb
CD       CD          0.00000  0.00000   A     3.39967e-01   3.59824e-01
; 1.91  0.0860 

#include "gbsa-local.itp"
#include "protein.itp"
#include "ligand.itp"


Obviously, I had to remove the atomtypes section from ligand.itp
directly into the top file and between the inculde force field line and
the ligand,itp file o make things work. I hope this helps someone out
there struggling with similar problems.

Vedat



Am 28.08.19 um 14:30 schrieb Mark Abraham:
> Hi,
>
> The answer is still the same - if gbsa.itp has the right contents, is it
> being included at the right time?
>
> Mark
>
> On Wed, 28 Aug 2019 at 12:57, Vedat Durmaz <vedat.durmaz at gmx.net> wrote:
>
>> 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
>>>
>>>
>>>
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