On Mon, Apr 16, 2018, Lorena.Rosaleny.uv.es wrote:
>
> 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:
It's not clear exactly what program you tried to compile and execute.
I've attached my version (bench_nm.nab), along with the output from
"./a.out gcn4p1". I hope this helps you find the problem.
> 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.
Again, since we don't know what output you really got, it's hard to say
whether something is wrong or not. You asked for 0 eigenvectory (eigp),
so you won't get a vecs file in that case.
...good luck....dac
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Received on Mon Apr 16 2018 - 06:00:06 PDT
