AMBER Archive (2008)

Subject: RE: AMBER: NAB examples

From: Hu, Shaowen (JSC-SK)[USRA] (Shaowen.Hu-1_at_nasa.gov)
Date: Mon Apr 07 2008 - 11:09:44 CDT

Thanks Dave. My file is:

molecule m;
float x[2000], f[2000], v[2000];
float dgrad, fret;
float t1,t2;
int ier;
file fp;

m = getpdb("gbrna.pdb");
readparm(m, "gbrna.prmtop");
fp=fopen("gbrna_long.mdcrd","w");
mm_options( "ntpr=100, ntwx=100, gb=1, kappa=0.10395, cut=99.0, diel=C,
tempi=300., rattle=0");
mme_init( m, NULL, "::Z", x, fp);

setxyz_from_mol( m, NULL, x );
t1 = second();
ier = md(3*m.natoms, 1000, x, f, v, mme );
t2 = second();
printf( "md returns %d; elapsed time was %8.3f\n", ier, t2-t1 );
putxv( "gbrna_long.x", "rattle md", m.natoms, 0.0, x, v );
fclose(fp);

I compiled with nobintraj option. But the file I obtained is not
readable as AMBER.

Thanks for your help,
Shaowen

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of David A. Case
Sent: Monday, April 07, 2008 10:33 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: NAB examples

On Mon, Apr 07, 2008, Hu, Shaowen (JSC-SK)[USRA] wrote:
>
> Thanks for your efforts for providing new tools for AMBER. I have
> trouble to generate trajectory for NAB MD. Could somebody kindly refer

> to some more examples?
>

It would be helpful if you said what you tried, and what the result was.

The final parameter to mme_init() give the file name for the trajectory
file; the "ntwx" paramter in mm_options gives the frequency at which the
trajectory is written.

Hope this helps....dac

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