[gmx-users] missing gbsa parameters

[Alan]

Have a look at http://code.google.com/p/acpype/wiki/TutorialAcpype4Gromacs

There there's a note:

*NB(1):* #include "Ligand.itp" has to be inserted right after
ffamber**.itp line
and before Protein_*.itp line in *Complex.top*.

Are you inserting your gbsa.itp in the *right* place of your top file?

Alan

On 4 May 2012 14:14, Vedat Durmaz <durmaz at zib.de> wrote:

>
> 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> 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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-- 
Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt - PANDA, EMBL-EBI
CB10 1SD, Hinxton, Cambridge, UK
+44 1223 49 4588
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