Hi there,
look at 'acpype -h', in particular:
-g, --disambiguatedisambiguate lower and uppercase atomtypes in GMX top
file
Alan
On 3 May 2012 14:34, Vedat Durmaz dur...@zib.de wrote:
hi guys,
i'm trying to simulate some receptor ligand system with implicit
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
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
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.
On 5/4/12 9:44 AM, Vedat Durmaz wrote:
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
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?
the order of force field, ligand, target is correct. and usually works
fine in explicit solvent simulations.
but i actually do not include the gbsa.itp, since it is defined by the
choice of the force field. (as soon as i rename its gbst.itp, grompp
says it cannot find that file ..)
but in
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
On 5/3/12 9:34 AM, Vedat Durmaz 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
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