[gmx-users] missing gbsa parameters

[Vedat Durmaz]

thanks justin and alan.

i also had the suspicion that the error is caused by case sensitivity. 
simply replacing all atom types from lower to upper case within the 
ligand.itp file yields the same error: "missing gb parameters".


using the "--disambiguate" option for the parameterization with acpype 
has exactly no effect. the generated *_GMX.itp file still contains the 
same lower case letters for each atom type. am i doing something wrong?


when using the "-atom amber" option (amber99sb instead of gaff), i do 
get upper case types, which are not always the same as given with "-a 
gaff". however, again, i am told by grompp, that GB parameters are 
missing for 15 atom types. and again, most of theese atom types ARE 
included in the respective gbsa.itp file (in 
share/gromacs/top/amber99sb.ff), but few are not.

and according to those atom types that are not mentioned in grompp's 
error output: about half of them is listed in gbsa.itp while the other 
ones are not.

i can't see any correlation between the atom types listed in my 
parameterized molecule's itp-file and the entries in gbsa.itp.

does anyone have any idea? is there perhaps some other force 
field/database file that is checked apart from gbsa.itp?!

thanks again,

vedat



Am 04.05.2012 11:23, schrieb 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 
> <mailto: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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