[gmx-users] missing gbsa parameters
durmaz at zib.de
Thu May 3 15:34:28 CEST 2012
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'
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
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