On Tue, 2014-03-11 at 10:38 +0100, Kanin Wichapong wrote:
> Dear AMBER Users,
>
>
> I tried to use PM6-DH+ or AM1-DH+ method for QM/MM-GBSA calculation.
> However, when I tried these methods, I got an error as:
>
>
> InputError: Invalid QM_THEORY (PM6-DH+)! This variable must be set to
> allowable options.
>
> See the AmberTools manual for allowable options.
>
> Exiting. All files have been retained.
>
>
>
> Here is an example of my input;
>
>
> input file for running PB and GB
>
> &general
>
> startframe=1,
>
> endframe=10,
>
> interval=1,
>
> verbose=2,
>
> keep_files=2,
>
> /
>
> &gb
>
> igb=5, ifqnt=1, qmcharge_com=0,
>
> qmcharge_lig=0, qmcharge_rec=0,
>
> qm_residues='634',
>
> qm_theory='PM6-DH+',
>
> /
>
>
> However, when I used just PM6 or AM1 method, the calculation was fine (no
> error).
>
>
> Moreover, I also tried to optimize the structure by using QM/MM method and
> using qm_theory='PM6-DH+' for energy minimization, and it worked fine (no
> error). So, I am not sure that the PM6-DH+ or AM1-DH+ method is implemented
> in the MMPBSA.py module or not. What can I do to solve this problems?
You can add 'PM6-DH+' to the list of recognized Hamiltonians in
MMPBSA.py or simply comment the section that checks the Hamiltonian out
of the script altogether (but then you lose a layer of error-checking).
The section of the code you're looking for is
$AMBERHOME/AmberTools/src/mmpbsa_py/MMPBSA_mods/main.py line 819. After
you update that module, you can run "make install" inside
$AMBERHOME/AmberTools/src/mmpbsa_py to reinstall MMPBSA.py.
Thanks,
Jason
P.S. The list of permissible Hamiltonians in QM/MMGBSA will be updated
for AmberTools 14 being released in about a month.
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 11 2014 - 05:30:03 PDT
