[gmx-users] missing gbsa parameters

Vedat Durmaz durmaz at zib.de
Thu May 3 15:34:28 CEST 2012

hi guys,

i'm trying to simulate some receptor ligand system with implicit solvent 
using gbsa in order to get a quick folding of some tens of N-terminal 
peptides. this works pretty well with the target only applying the 
amber99sb FF. as soon as i try to simulate it together with the ligand 
which was parameterized with acpype (using amber-antechamber), i get the 
following error at the grompp step:

GB parameter(s) missing or negative for atom type 'cc'
GB parameter(s) missing or negative for atom type 'n'
Fatal error:
Can't do GB electrostatics; the implicit_genborn_params section of the 
forcefield is missing parameters for 15 atomtypes or they might be negative.

the atom types in the error output are exactly those listed in the [ 
atom types ] section of the ligand's topology file created with 
acpype/antechamber. however, the atom types mentioned here ARE listed in 
the respective gbsa.itp file which looks like this:

[ implicit_genborn_params ]

; atype      sar      st     pi       gbr       hct
CC           0.172    1      1.554    0.1875    0.72 ; C

does anybody know how to handle this problem?

and is there someone that can tell me how (with which parameter values) 
to add GAFF atom types like e.g. "ss", "hn", "hx", "os" to the gbsa.itp 

thanks in advance and take care

vedat durmaz

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