yes, i do understand this. but what i really do not get is that grompp
fails telling me "GB parameter(s) missing or negative for atom type
'C'", ALTHOUGH 'C' is listed in gbsa.itp.
thus, from 15 atom types reportedly lacking gb parameters according to
grompp, about 10 ARE listed in gbsa.itp.
any idea what might cause that?
Am 04.05.2012 15:26, schrieb Justin A. Lemkul:
On 5/4/12 9:14 AM, Vedat Durmaz 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?!
With respect to GB parameters, only gbsa.itp is checked; there is no
auxiliary source of information. If any atom type is not listed
there, grompp will fail, as you're seeing. For any missing atom type,
you need to add appropriate parameters for it into gbsa.itp. This may
be trivial (redundancy in some atom types) or it may be difficult
(deriving new parameters that are compatible with the parent force
field).
-Justin
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