Hello,
My question is related to a a previously established thread (see below) started by Ella Gale in 2017.
I'd like to calculate normal modes for a simple protein, and I'm trying to use the approach suggested by David Case, with the code shown on Amber17 manual page 833 (section 39.4 Second derivatives and normal modes). I downloaded the gcn4p1.mc.pdb from the $AMBEHROME/AmberTools/benchmarks/nab/benchamarks/nab/ directory but got this when executing:
/a.out
mm_options: cut=999.
mm_options: ntpr=50
mm_options: nsnb=99999
mm_options: diel=C
mm_options: gb=1
mm_options: dielc=1.0
Violación de segmento (`core' generado)
I also tried to use the script bench_nr.nab with the gcn4p1 example. I used the pdb, top and x files from $AMBEHROME/AmberTools/benchmarks/nab/benchamarks/nab/. I added to the end of the script the same line that is described in the manual to calculate normal modes ( nmodes( x, 3*m.natoms, mme2, 0, 0, 0.0, 0.0, 0)), but I got a stdout that didn't seem to contain the full information on the normal modes (reduced mass, frequency and displacement vectors for each atom). I was expecting a vecs file, but didn't get one.
Any help is appreciated, thanks.
Lorena
------------------------------------------------------
Re: [AMBER] Simple normal mode analysis in amber
From: David Case <david.case.rutgers.edu>
Date: Sat, 7 Jan 2017 18:09:10 -0500
On Sat, Jan 07, 2017, Ella Gale wrote:
>
> I am trying to get the normal modes of simple chemicals (like hexane,
> benzene) in vacuo. I've spent hours looking through the tutorials, the
> internet and the manuals for both amber 2016 and 2015. I can see there is a
> lot of information there and some mention of normal modes, but all I want
> to do is take a structure built in leap, use a simple forcefield, minimise
> it (I know how to do all those steps) and then calculate the normal modes
> and output them to a file.
>
> How should I do it? Which program is best? Does anyone have any example
> code for this? I really expect it to be a two liner, so if anyone can give
> me those two lines or point me in the right direction, I would be very
> grateful.
It is indeed a very short program to compute normal modes. See examples
here:
$AMBERHOME/test/nab/Run.nmode{1,2,3}
There is also a complete example in Section 40.4 of the Amber 2016 Reference
Manual (entitled "Second derivatives and normal modes.") OK, this is 17
lines, but this example reads in the molecule information, carries out the
minimization, and then computes the normal modes (on line 17). So only one
line of code is really involved in computing normal modes.
For a more realisitic example:
$AMBEHROME/AmberTools/benchmarks/nab/benchamarks/nab/bench_nr.nab
(you will have to add a call to nmode() to the nab program in the second
example.
..hope this helps....dac
--
--
Lorena E. Rosaleny Peralvo, Senior Postdoctoral Researcher
Telf. +0034 963 544 418
Instituto de Ciencia Molecular
Universitat de València
c/ Catedrático José Beltrán Martínez nº 2
46980 Paterna (València)
SPAIN
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Received on Sun Apr 15 2018 - 23:30:02 PDT
