Re: [AMBER] hoogsteen base pair

From: Martina Devi <martinadevi2011.gmail.com>
Date: Fri, 1 Apr 2016 20:55:28 +0530

Dear Amber Users

I used the given command to create a hoogsten base pair for Guanine but the
pdb which is generated does not have the hoogsten base pair but shows a
watson crick base pair. Though the pdb gets generated it shows

title:
default_name
useboundsfrom: atom mismatch:m1(13) & m2(0)
useboundsfrom set bounds for 0 atoms

May I know if there is any mistake with the input.

molecule m;
bounds b;

m = fd_helix( "arna", "g", "rna");
b = newbounds ( m, "ag.1X.pdb");

useboundsfrom(b, m, "1:1,5:??,H?
T]",getpdb("/root/home/Amber12/amber12/dat/dgdb/basepairs/ag.IX.pdb"),"::,H?[
T]",0.1);
useboundsfrom(b, m, "1:2,6:??,H?
T]",getpdb("/root/home/Amber12/amber12/dat/dgdb/basepairs/ga.IX.pdb"),"::,H?[
T]",0.1);

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

The c file :

#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;
static STRING_T *__st0001__ = NULL;
static STRING_T *__st0002__ = NULL;
static STRING_T *__st0003__ = NULL;
m = fd_helix( STEMP( __st0001__, "arna" ), STEMP( __st0002__, "g" ), STEMP(
__st0003__, "rna" ) );
b = newbounds( m, "ag.1X.pdb" );

useboundsfrom( b, m, "1:1,5:??,H? T]", getpdb(
"/root/home/Amber12/amber12/dat/dgdb/basepairs/ag.IX.pdb", NULL ), "::,H?[
T]", 1.000000E-01 );
useboundsfrom( b, m, "1:2,6:??,H? T]", getpdb(
"/root/home/Amber12/amber12/dat/dgdb/basepairs/ga.IX.pdb", NULL ), "::,H?[
T]", 1.000000E-01 );

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


      exit( 0 );
}
Is there any error?

I am attaching my pdb file

Thanks in advance
Martina

On Fri, Apr 1, 2016 at 8:53 PM, Martina Devi <martinadevi2011.gmail.com>
wrote:

> Dear Amber Users
>
> I used the given command to create a hoogsten base pair for Guanine but
> the pdb which is generated does not have the hoogsten base pair but shows a
> watson crick base pair. Though the pdb gets generated it shows
>
> title:
> default_name
> useboundsfrom: atom mismatch:m1(13) & m2(0)
> useboundsfrom set bounds for 0 atoms
>
> May I know if there is any mistake with the input.
>
> molecule m;
> bounds b;
>
> m = fd_helix( "arna", "g", "rna");
> b = newbounds ( m, "ag.1X.pdb");
>
> useboundsfrom(b, m, "1:1,5:??,H?
> T]",getpdb("/root/home/Amber12/amber12/dat/dgdb/basepairs/ag.IX.pdb"),"::,H?[
> T]",0.1);
> useboundsfrom(b, m, "1:2,6:??,H?
> T]",getpdb("/root/home/Amber12/amber12/dat/dgdb/basepairs/ga.IX.pdb"),"::,H?[
> T]",0.1);
>
> putpdb( "b.pdb", m, "-wwpdb");
>
> The c file :
>
> #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;
> static STRING_T *__st0001__ = NULL;
> static STRING_T *__st0002__ = NULL;
> static STRING_T *__st0003__ = NULL;
> m = fd_helix( STEMP( __st0001__, "arna" ), STEMP( __st0002__, "g" ),
> STEMP( __st0003__, "rna" ) );
> b = newbounds( m, "ag.1X.pdb" );
>
> useboundsfrom( b, m, "1:1,5:??,H? T]", getpdb(
> "/root/home/Amber12/amber12/dat/dgdb/basepairs/ag.IX.pdb", NULL ), "::,H?[
> T]", 1.000000E-01 );
> useboundsfrom( b, m, "1:2,6:??,H? T]", getpdb(
> "/root/home/Amber12/amber12/dat/dgdb/basepairs/ga.IX.pdb", NULL ), "::,H?[
> T]", 1.000000E-01 );
>
> putpdb( "b.pdb", m, "-wwpdb" );
>
>
> exit( 0 );
> }
> Is there any error?
>
> Thanks in advance
> Martina
>


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Received on Fri Apr 01 2016 - 08:30:06 PDT
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