AMBER Archive (2008)

Subject: Re: AMBER: nab

From: Alessandro Nascimento (al.s.nascimento_at_gmail.com)
Date: Mon May 12 2008 - 19:59:27 CDT

I used nab recently to minimize a (bad!) protein structure.

My min.nab input file was :
//*************************************************************
/teste
molecule m;
int ier;
float m_xyz[ dynamic ], f_xyz[ dynamic ], v[ dynamic ];
float dgrad, fret, dummy[2];
float time1, time2, time3, time4;
time1=second();
m = getpdb_prm ( "delphi.pdb",
"/usr/local/amber9/dat/leap/cmd/leaprc.ff99SB", "", 0); // Defines a
initial PDB and a FF

allocate m_xyz[ 3*m.natoms ]; allocate f_xyz[ 3*m.natoms ];
allocate v[ 3*m.natoms ];
setxyz_from_mol(m, NULL, m_xyz);

mm_options("cut=25.0, ntpr=5, nsnb=999, gamma_ln=5.0, gb=1, diel=C,
gbsa=1, surften=0.005,"); // MD options as in amber
mme_init(m, NULL, "::ZZZ", dummy, NULL);
fret = mme(m_xyz, f_xyz, 1);
printf ("Initial energy: %8.3f\n", fret);
time2=second();
printf("Elapsed time: %8.3f seconds\n", time2-time1);
dgrad=0.1;
ier=conjgrad(m_xyz, 3*m.natoms, fret, mme, dgrad, 10.0, 350);
time3=second();
printf("Total elapsed time: %8.3f seconds\n", time3-time1);
setxyz_from_mol(m, NULL, m_xyz);
putpdb("minimized.pdb", m);
time4=second();
printf("Total execution time: %8.3f seconds\n", time4-time1);
//*************************************************************

This file can be compiled with nab using:

% nab -O -o min.x nab.min

This will create a min.x executable, which can be executed just typing './min.x'

The commands in the nab file are very simple and are detailed in
AmberTools manual.
 You can, of course, change to fit your purposes.

In my file, the input pdb file "delphi.pdb" will be minimized in 350
steps of conjugate gradient and energies will be printed on
each 5 steps. There is some timing stuff there also and a final pdb
"minimized.pdb" will be written in the end of the minimization run
with the final coordinates.

Pg 204 of AmberTools has a similar example with some explanation you
might want to have a look as well!

And, of course, you can also use nab for a number of purposes other
than protein energy minimization and dynamics....

Hope this helps....

--alessandro

On Mon, May 12, 2008 at 5:40 PM, Rabin <ab_study_at_yahoo.com> wrote:
> can any one provide me the way to run a nab script? I am really confused
> about the way nab works. I thiink the tutorial doesn't tell about how to run
> it (may be I am wrong).I will be very much thankful if someone provide me a
> protocal to run nab.
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu