2011/9/21 Marek Maly <marek.maly.ujep.cz>
>
> Jason thanks a lot again !
>
> This is really incredible service ! No way to move from Amber :))
>
> What is still not so clear is the easest way how to incorporate scee = 1.2
> into
> nmode calculation.
>
> I succeeded with this method which doesn.t require changing C/F sources
> /recompiling of Amber:
>
> I just "hacked" file
>
> mm_pbsa_createinput.pm
>
> by adding line:
>
> print OUT " scee= 1.2,\n";
>
> to relevant block:
>
>
> $name = "nmode" . $suf . ".in";
> open(OUT,">$name") || die(" $name not opened\n For details see:
> $HTMLPATH#create_nmode_nmodein_not_opened\n");
> print OUT "File generated by mm_pbsa.pl\n";
> print OUT " &data\n";
> print OUT " ntx = 0,\n"; # Binary format is no longer supported
> print OUT " ntrun = 1, nvect = $nvect,\n";
> print OUT " drms = $nmdrms,\n";
> print OUT " dielc = 4.0, idiel = 0,\n";
> print OUT " idecomp= $idecomp,\n";
> print OUT " scee= 1.2,\n";
> print OUT " &end\n";
> print OUT "END\n";
> close(OUT);
>
That should work as well. I was suggesting changing the source code simply
because 2.0 is no longer used anywhere that I've seen in the Amber force
fields (I never even knew that it once was), so there's not much point in
keeping 2.0 as a default anymore.
However, nmode is deprecated and is no longer developed (maybe it'll just be
removed from Amber altogether someday? I'm not sure...)
>
> however especially for those who have not so easy possibility to change
> Amber files (i.g. users of supercomputer centers ... ) might be useful
> some another way with no necessity to change Amber sources.
>
> So is it possible:
>
> a)
> to run mm_pbsa.pl using "by hand" created sandmin*.in nmode*.in files
> instead regular mm_pbsa.in file ?
>
> With regular input file, the syntax to run MMPBSA calculation is:
>
> mm_pbsa.pl mm_pbsa.in > mm_pbsa.out
>
> So using sandmin*.in nmode*.in should be similar to:
>
> mm_pbsa.pl sandmin*.in nmode*.in > mm_pbsa.out
>
> but if using exactly this form it doesn.t work.
>
Yes, because mm_pbsa.pl expects an mm_pbsa.pl-specific input file. Not
input files to use for the calculations.
>
> b)
> Another possibility might be to start mm_pbsa by regular way but with the
> condition:
>
> "Please do not create sandmin*.in nmode*.in files but use that which are
> already in actual directory"
>
> If I am not wrong something like this is possible in mmpbsa.py just by
> setting some parameter but
> I am not aware of the same possibility in case of mm_pbsa.pl.
>
As far as I know that functionality exists only in MMPBSA.py. I think that
mm_pbsa.pl *does* have an option to use a nab program for normal mode
calculations rather than using nmode itself, which may be a better option in
this case. It would be detailed in the Amber 11 manual if that option is
available. We (the people that typically respond to MM/PBSA questions on
the list) don't really support the perl version of MM/PBSA (which was part
of the motivation behind developing the python version in the first place).
We answer questions when we can, but don't actually participate in its
continued development. That's why we continue to suggest MMPBSA.py as an
alternative and are unlikely to contribute further developments to the perl
version.
All the best,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 21 2011 - 22:00:02 PDT
