CRAIG ANTHONY MARHEF wrote:
>
> Hello everyone,
>
> I have a question concerning the Amber Interface and using the torsion driver
> that is posted in the FAQ's on the amber page.
>
> I am using amber 5.0 and From what I can gather the interface is also v5.
> I get an error in the *.out file which says that the option "NMRMAX no longer
> supported" . Is there a way to prevent the interface from writing this option
> in the input file?
This problem results from a bug in Sander version 5, whereby the code
was not made backward compatible with NMRMAX. A bugfix was sent out about
how to fix this problem in Sander itself. But as for using Interface, you
can also make a couple of trivial changes to the interface code to
fix the problem.
Go to the ../amber5/interface/def directory, edit the sander_namelist.def
file and make the following two changes (first line is NEW code; second
line is OLD code):
"taur = <TAUR>" ,"nmropt = <NMROPT>","isftrp = <ISFTRP>",\
"taur = <TAUR>" ,"nmrmax = <NMRMAX>","isftrp = <ISFTRP>",\
if (nmropt.eq.2 .or. nmropt.eq.3) then
if (nmrmax.eq.2 .or. nmrmax.eq.3) then
Then re-process the Interface script using install_ambint in the
../amber5/interface directory.
> Also there seems to be a bug in the run section for the *.restart file I have
> had to add the -r flag as part of the input to get sander to recoganize the
> text put after /restrt = option.
>
> For example "run / restrt = restart_file.xyz" give an error when sander runs
> saying that restart_file.xyz is an unrecognized sander control option.
> But if I change it to "run / restrt = "-r restart_file.xyz"" sander
> recoganizes restart_file.xyz as the restart file.
>
> A general question concerning this script. What do the "" signify below(ie
> after inpcrd="" or prmtop="").
ARGH! Something is wrong with the example that is posted on the Web
site! Constructs such as
assign inpcrd = "<coord>"
have turned into
assign inpcrd = ""
which is why things don't seem to make sense (and probably is why
you are having other problems!)
Fortunately, the sample torsional driver, in the CORRECT form, is
available in the interface examples directory, as file minloop.example:
../amber5/interface/examples/minloop.example
Hope this helps,
dap
--
David A. Pearlman email: dap_at_vpharm.com
Vertex Pharmaceuticals Inc.
130 Waverly St. "There are only 25 great people in the world &
Cambridge, MA 02139-4242 5 of them are hamburgers..." -- Cptn Beefheart
Received on Mon Oct 18 1999 - 17:03:52 PDT
