On Tue, 2014-07-29 at 22:56 +0800, xy21hb wrote:
> Dear all,
>
>
> I wonder if there is anywhere I can know the details of .in files used
> for normal mode analysis.
> I understand from the maunal that it needs steepest descent, conjugate
> gradient,... in ".in" files,
> but I am not sure about other parameters set in these different
> stages, esp. the enregy tolerance to obtain a global minimum
> structure.And I need all the modes for further analysis, not just only
> the first 50 modes or so.
Do you have any specific questions? The question "how do I run normal
mode calculations" is not an easy question to answer over email. I
suggest writing a NAB program to run a normal mode calculation (rather
than the 'nmode' program). You can see a sample program in chapter 37
section 4 (page 714) of the Amber 14 manual. There is also a sample
program that does minimization using the "xmin" minimizer (which usually
does a better job than conjgrad) in
$AMBERHOME/AmberTools/src/mmpbsa_py/mmpbsa_entropy.nab).
You can specify how many eigenmodes you want printed via the "eigp" flag
(just specify as many eigenmodes as your molecule has if you want all of
them).
As far as the minimization tolerance goes, the smaller you can afford
the better. MMPBSA.py assigns a default of 0.001 when performing normal
mode entropy calculations. However, you may need one or two orders of
magnitude smaller for your application.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Jul 29 2014 - 08:30:03 PDT
