[gmx-users] missing gbsa parameters

[Alan]

Hi there,

look at 'acpype -h', in particular:

 -g, --disambiguate    disambiguate lower and uppercase atomtypes in GMX top
                        file

Alan

On 3 May 2012 14:34, Vedat Durmaz <durmaz at zib.de> 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
>
>
> 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?
>
> thanks in advance and take care
>
> vedat durmaz
>
>
>
>
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-- 
Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt - PANDA, EMBL-EBI
CB10 1SD, Hinxton, Cambridge, UK
+44 1223 49 4588
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