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 <dur...@zib.de
<mailto:dur...@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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