[gmx-users] missing gbsa parameters

Justin A. Lemkul jalemkul at vt.edu
Thu May 3 15:45:49 CEST 2012

On 5/3/12 9:34 AM, Vedat Durmaz wrote:
> 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

Atom types are case-sensitive, thus "cc" and "CC" are not, in fact, the same.

> 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 file?

You can probably assign the atom types you need based on chemical similarity to 
existing atom types/functional groups.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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