On Fri, Jun 12, 2015 at 2:40 AM, Debodyuti Dutta <dutta.debodyuti.gmail.com>
wrote:
> Dear AMBER user,
>
> I am trying to run MMPBSA on my system which has two zinc ions (paameter
> files prepared from CHAMBER) . For my purpose I want to set sasopt=1. My
> input file looks
> like:-
> Input file for running PB
> &general
> endframe=1000, verbose=1,
> entropy=0
> /
> &pb
> inp=1, radiopt=0, istrng=0.150, saopt= 1,
> /
> &decomp
> idecomp=1, print_res="1-380"
> dec_verbose=1,
> /
>
> The calculation gives the following error:-
> InputError: Unknown variable sasopt in &pb
>
As the error message states, sasopt is not a supported input variable in
MMPBSA.py. You need to use PBSA directly to access this variable.
An alternative approach is to create template mdin files (using the
-make-mdins flag), add the sasopt=1 option to the &pb section of the
generated _MMPBSA_*.mdin files, and then re-run the MMPBSA.py command with
-use-mdins instead of -make-mdins.
Note sasopt is only supported through sander, so you would normally have to
set use_sander=1 in the &general section of the MMPBSA.py input file, but
chamber prmtop files force the use of sander, anyway.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Jun 12 2015 - 03:00:03 PDT
