Hi Rasha,
Given the error that you posted in your previous email, I would assume that
you did not explicitly call *mmpbsa_py_nabmode* but instead used *MMPBSA.py*
?* *In order to use *mmpbsa_py_nabmode* you need to supply the following in
the order specified below:
Usage: mmpbsa_py_nabnmode {pdb} {prmtop} {maxiter} {drms} {'string of MM
options'} {nc/trj}
maxiter= maximum number of iterations to perform during the minimization,
drms= is the convergence criterion for the minimization, {'string of MM
options'} and example would be "cut=999., ntpr=50, nsnb=99999, diel=C,
gb=1, dielc=1.0", look into the AmberTools manual in the nab section for
more MM options if you have any questions. and (nc/trj)= program either
reads in netcdf/ASCII formatted trajectories..
Hope that helps...
On Wed, Feb 20, 2013 at 10:27 AM, Rasha Alqus
<rasha.alqus.manchester.ac.uk>wrote:
> Dear Amber user,
>
>
>
> when am trying to use mmpbsa_py_nabnmode programme to calculate the
> normal modes,
>
> i have only a single macromolecule, no ligand or receptor, when i
> submitted a job an error came back that the ligand and receptor topology
> file doesn't exists. How I can use mmpbsa_py_nabnmode for only a single
> macromolecule not a complex.
>
>
>
> Regards
>
>
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>
--
T. Dwight McGee Jr.
Quantum Theory Project
University of Florida
Graduate Student
dwight.mcgee.gmail.com
"Problems cannot be solved at the same level of awareness that created
them."
Albert Einstein
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Received on Wed Feb 20 2013 - 08:30:04 PST
