[gmx-users] missing gbsa parameters
durmaz at zib.de
Fri May 4 15:14:53 CEST 2012
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?!
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
> 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
> 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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