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 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
Atom types are case-sensitive, thus "cc" and "CC" are not, in fact, the same.
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?
You can probably assign the atom types you need based on chemical similarity to
existing atom types/functional groups.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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