Re: [AMBER] Creating hoogsteen basepaired DNA using NAB

From: Andre Serobian <a.serobian.unsw.edu.au>
Date: Sat, 9 Jul 2011 11:38:01 +1000

Hi David,

Thankyou for the help, I made the changes you suggested with the following results:


error message:
...................................................................................................................................................................................................................................
"9 syntax error nab2c failed!"
...................................................................................................................................................................................................................................





nad file:
...................................................................................................................................................................................................................................
molecule m;
bounds b;

m = fd_helix( "abdna", "atgcat", "dna" );
b = newbounds ( m, "at.XXIII.pdb");

useboundsfrom(b, m, "1:1,5:??,H?T]",getpdb( /usr/local/amber11/dat/dgdb/basepairs + "at.XXIII.pdb" ),"::??,H?[T]",0.1);
useboundsfrom(b, m, "1:2,6:??,H?T]",getpdb( /usr/local/amber11/dat/dgdb/basepairs + "ta.XXIII.pdb" ),"::??,H?[T]",0.1);

putpdb( "nuch.pdb", m, "-wwpdb");
...................................................................................................................................................................................................................................




and the .c file looks like this:
...................................................................................................................................................................................................................................
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <math.h>
#include <assert.h>
#include "nabcode.h"
extern char NAB_rsbuf[];
static int mytaskid, numtasks;

static MOLECULE_T *m;

static BOUNDS_T *b;


int main( argc, argv )
        int argc;
        char *argv[];
{
        nabout = stdout; /*default*/

        mytaskid=0; numtasks=1;
m = fd_helix( STEMP( __st0001__, "abdna" ), STEMP( __st0002__, "atgcat" ), STEMP( __st0003__, "dna" ) );
b = newbounds( m, "at.XXIII.pdb" );
...................................................................................................................................................................................................................................

I am not seeing the "get" error anymore but now there is some type of "syntax" error, any ideas would be great, thankyou.

Kind regards,

Andre



________________________________________
From: case [case.biomaps.rutgers.edu]
Sent: Friday, 8 July 2011 10:41 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Creating hoogsteen basepaired DNA using NAB

On Fri, Jul 08, 2011, Andre Serobian wrote:

> molecule m;
> bounds b;
>
> m = fd_helix( "abdna", "atgcat", "dna" );
> b = newbounds ( m, "at.XXIII.pdb");
>
> useboundsfrom(b, m, "1:1,5:??,H?T]", get-pdb( PATH + "at.XXIII.pdb" ), "::??,H?[T]", 0.05 );

You want "getpdb", not "get-pdb". Be sure that PATH is somehow expanded
to a valid string: easiest is just to spell out the entire path, or copy
the at.XXIII.pdb file to the local directory. [I see that the example on
p. 313 has a hypenation error caused by the formatting program.]

It is also true that NAB is not all that helpful when there are syntax errors
in the code. A common strategy is to look at the end of .c file, in order to
get some more clue about what is going on.

...hope this helps...dac


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Received on Fri Jul 08 2011 - 19:00:04 PDT
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